3j5l - Revision history

OCA at 14:15, 24 January 2024

OCA — Wed, 24 Jan 2024 14:15:53 GMT

←Older revision		Revision as of 14:15, 24 January 2024
Line 3:		Line 3:
	<SX load='3j5l' size='340' side='right' viewer='molstar' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>		<SX load='3j5l' size='340' side='right' viewer='molstar' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j5l]] is a 33 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Escherichia_coli~~ Escherichia coli] and [https://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J5L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j5l]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J5L FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>~~, ~~<scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 6.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [https://pdbe.org/3j5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [https://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [https://pdbe.org/3j5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [https://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[https://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[https://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[https://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[https://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[https://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[https://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[https://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[https://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[https://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[https://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[https://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[https://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[https://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[https://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[https://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[https://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[https://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[https://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[https://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[https://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>	+	[https://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Escherichia coli]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Streptococcus sanguinis]]		[[Category: Streptococcus sanguinis]]
-	[[Category: Arenz, S]]	+	[[Category: Arenz S]]
-	[[Category: Beckmann, R]]	+	[[Category: Beckmann R]]
-	[[Category: Berninghausen, O]]	+	[[Category: Berninghausen O]]
-	[[Category: Gupta, P]]	+	[[Category: Gupta P]]
-	[[Category: Mankin~~, A S~~]]	+	[[Category: Mankin AS]]
-	[[Category: Ramu, H]]	+	[[Category: Ramu H]]
-	[[Category: Vazquez-Laslop, N]]	+	[[Category: Vazquez-Laslop N]]
-	[[Category: Wilson~~, D N]]~~	+	[[Category: Wilson DN]]
-	~~[[Category: Erythromycin]]~~	+
-	~~[[Category: Ribosome-antibiotic complex]]~~	+
-	~~[[Category: Stalling~~]]	+

OCA at 03:50, 21 April 2022

OCA — Thu, 21 Apr 2022 03:50:12 GMT

←Older revision		Revision as of 03:50, 21 April 2022
Line 3:		Line 3:
	<SX load='3j5l' size='340' side='right' viewer='molstar' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>		<SX load='3j5l' size='340' side='right' viewer='molstar' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j5l]] is a 33 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [~~http~~://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3J5L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j5l]] is a 33 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J5L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [~~http~~://pdbe.org/3j5l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [https://pdbe.org/3j5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [https://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[~~http~~://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[~~http~~://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[~~http~~://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[~~http~~://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[~~http~~://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[~~http~~://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[~~http~~://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[~~http~~://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[~~http~~://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[~~http~~://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[~~http~~://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[~~http~~://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[~~http~~://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[~~http~~://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[~~http~~://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[~~http~~://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[~~http~~://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[~~http~~://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[~~http~~://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[~~http~~://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>	+	[[https://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[https://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[https://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[https://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[https://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[https://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[https://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[https://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[https://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[https://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[https://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[https://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[https://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[https://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[https://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[https://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[https://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[https://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[https://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[https://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[https://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 17:57, 10 April 2020

OCA — Fri, 10 Apr 2020 17:57:14 GMT

←Older revision		Revision as of 17:57, 10 April 2020
Line 3:		Line 3:
	<SX load='3j5l' size='340' side='right' viewer='molstar' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>		<SX load='3j5l' size='340' side='right' viewer='molstar' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j5l]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3J5L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j5l]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J5L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [http://pdbe.org/3j5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [http://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [http://pdbe.org/3j5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [http://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 17:24, 6 March 2020

OCA — Fri, 06 Mar 2020 17:24:10 GMT

←Older revision		Revision as of 17:24, 6 March 2020
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Structure of the E. coli 50S subunit with ErmBL nascent chain==		==Structure of the E. coli 50S subunit with ErmBL nascent chain==
-	<~~StructureSection~~ load='3j5l' size='340' side='right' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>	+	<SX load='3j5l' size='340' side='right' viewer='molstar' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j5l]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J5L FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j5l]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J5L FirstGlance]. <br>
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [http://pdbe.org/3j5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [http://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [http://pdbe.org/3j5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [http://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/~~RL15_ECOLI RL15_ECOLI~~]] ~~This protein binds the 5S rRNA. It is required for the late stages~~ of ~~subunit~~ assembly, ~~and is essential for 5S~~ rRNA assembly ~~onto~~ the ~~ribosome~~.[HAMAP-Rule:~~MF_01341_B~~] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/~~RL19_ECOLI RL19_ECOLI~~]] This protein ~~is located~~ at the ~~30S-50S~~ ribosomal ~~subunit interface~~. In the ~~70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S~~ subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, ~~it is probably also mobile. Required for association of the 30S~~ and ~~50S subunits to form~~ the ~~70S ribosome, for~~ tRNA binding ~~and peptide bond formation. It has been suggested to have~~ peptidyltransferase ~~activity; this is highly controversial~~.[HAMAP-Rule:~~MF_01320_B~~] ~~In the E.coli 70S ribosome~~ in ~~the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G~~.[HAMAP-Rule:~~MF_01320_B~~] [[http://www.uniprot.org/uniprot/~~RL17_ECOLI RL17_ECOLI~~]] ~~Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this~~ protein ~~initially~~ binds ~~near~~ the ~~5'-end of the 23S~~ rRNA. It is ~~important during~~ the ~~early~~ stages of ~~50S~~ assembly~~. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit~~ and ~~ribosome.<ref>PMID:2442760</ref> Protein L4~~ is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ~~ribosome~~ assembly ~~(residues 89-103).<ref>PMID:2442760</ref> Forms part of~~ the ~~polypeptide exit tunnel~~.~~<ref>PMID~~:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/~~RL18_ECOLI RL18_ECOLI~~]] This is ~~one of~~ the ~~proteins that mediates the attachment of the 5S rRNA subcomplex onto the large~~ ribosomal subunit ~~where it forms part of~~ the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome~~-bound tRNAs.<ref>PMID~~:~~353728</ref> [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins,~~ it ~~binds directly~~ to the ~~5'-end of the 23S~~ rRNA~~, where it nucleates assembly~~ of the ~~50S~~ subunit~~. It is not thought to be involved in the functions~~ of ~~the mature 50S subunit in vitro~~.~~<ref>PMID:357435</ref> One of~~ the ~~proteins that surrounds the polypeptide exit tunnel on the outside of the subunit~~.~~<ref>PMID~~:~~357435</ref> [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near~~ the ~~3'-end of the 23S~~ rRNA~~, where it nucleates assembly of the 50S subunit~~.~~[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This~~ protein ~~binds directly to at least 2 domains of the 23S ribosomal RNA, thus~~ is ~~important in its secondary structure. It is located near~~ the ~~subunit interface in the base of the L7/L12 stalk~~, ~~and near the tRNA binding site of the peptidyltransferase center~~.[HAMAP-Rule:~~MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365~~] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>	+	[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
	[[Category: Streptococcus sanguinis]]		[[Category: Streptococcus sanguinis]]
	[[Category: Arenz, S]]		[[Category: Arenz, S]]

OCA at 08:12, 18 July 2018

OCA — Wed, 18 Jul 2018 08:12:12 GMT

←Older revision		Revision as of 08:12, 18 July 2018
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	{{Large structure}}		{{Large structure}}
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B~~] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368~~] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/~~RL3_ECOLI RL3_ECOLI~~]] ~~One~~ of ~~two~~ assembly ~~inititator proteins~~, ~~it binds directly near the 3'-end of the 23S~~ rRNA~~, where it nucleates~~ assembly of the ~~50S subunit~~.[HAMAP-Rule:~~MF_01325_B~~] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/~~RL6_ECOLI RL6_ECOLI~~]] This protein ~~binds directly to~~ at ~~least 2 domains of~~ the ~~23S~~ ribosomal ~~RNA, thus is important in its secondary structure~~. ~~It is located near~~ the subunit ~~interface in~~ the base of the ~~L7/L12~~ stalk, and ~~near~~ the tRNA binding ~~site of the~~ peptidyltransferase ~~center~~.[HAMAP-Rule:~~MF_01365~~] ~~Gentamicin-resistant mutations~~ in ~~this protein affect translation fidelity~~.[HAMAP-Rule:~~MF_01365~~] [[http://www.uniprot.org/uniprot/~~RL15_ECOLI RL15_ECOLI~~]] ~~This~~ protein binds the 5S rRNA. It is ~~required for~~ the ~~late~~ stages of ~~subunit~~ assembly, and is ~~essential~~ for ~~5S rRNA~~ assembly ~~onto~~ the ~~ribosome~~.~~[HAMAP-Rule~~:~~MF_01341_B]~~ [[http://www.uniprot.org/uniprot/~~RL19_ECOLI RL19_ECOLI~~]] This ~~protein~~ is ~~located at~~ the ~~30S-50S~~ ribosomal subunit ~~interface. In~~ the ~~70S~~ ribosome ~~(PubMed~~:~~12809609)~~ it ~~has been modeled~~ to ~~make two contacts with~~ the ~~16S~~ rRNA of the ~~30S~~ subunit ~~forming part~~ of ~~bridges B6 and B8~~. In the 3.~~5 A resolved structures (PubMed~~:~~16272117) L14 and L19 interact and together make contact with~~ the ~~16S~~ rRNA. ~~The~~ protein ~~conformation~~ is ~~quite different between~~ the ~~50S and 70S structures~~, ~~which may be necessary for translocation~~.[HAMAP-Rule:~~MF_00402~~] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>	+	[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 04:12, 5 August 2016

OCA — Fri, 05 Aug 2016 04:12:24 GMT

←Older revision		Revision as of 04:12, 5 August 2016
Line 1:		Line 1:
		+	{{Large structure}}
	==Structure of the E. coli 50S subunit with ErmBL nascent chain==		==Structure of the E. coli 50S subunit with ErmBL nascent chain==
	<StructureSection load='3j5l' size='340' side='right' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>		<StructureSection load='3j5l' size='340' side='right' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [http://www.ebi.ac.uk/pdbsum/3j5l PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [http://pdbe.org/3j5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [http://www.ebi.ac.uk/pdbsum/3j5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j5l ProSAT]</span></td></tr>
	</table>		</table>
		+	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>		[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>
Line 17:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3j5l" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:44, 25 December 2014

OCA — Thu, 25 Dec 2014 15:44:02 GMT

←Older revision		Revision as of 15:44, 25 December 2014
Line 1:		Line 1:
-	~~{{Large structure}}~~	+	==Structure of the E. coli 50S subunit with ErmBL nascent chain==
-	~~{{STRUCTURE_3j5l\| PDB=3j5l \| SCENE= }}~~	+	<StructureSection load='3j5l' size='340' side='right' caption='[[3j5l]], [[Resolution\|resolution]] 6.60Å' scene=''>
-	===Structure of the E. coli 50S subunit with ErmBL nascent chain===	+	== Structural highlights ==
-	~~{{ABSTRACT_PUBMED_24662426}}~~	+	<table><tr><td colspan='2'>[[3j5l]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J5L FirstGlance]. <br>
-		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
-	==Function==	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3j5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j5l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j5l RCSB], [http://www.ebi.ac.uk/pdbsum/3j5l PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>		[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In bacteria, ribosome stalling during translation of ErmBL leader peptide occurs in the presence of the antibiotic erythromycin and leads to induction of expression of the downstream macrolide resistance methyltransferase ErmB. The lack of structures of drug-dependent stalled ribosome complexes (SRCs) has limited our mechanistic understanding of this regulatory process. Here we present a cryo-electron microscopy structure of the erythromycin-dependent ErmBL-SRC. The structure reveals that the antibiotic does not interact directly with ErmBL, but rather redirects the path of the peptide within the tunnel. Furthermore, we identify a key peptide-ribosome interaction that defines an important relay pathway from the ribosomal tunnel to the peptidyltransferase centre (PTC). The PTC of the ErmBL-SRC appears to adopt an uninduced state that prevents accommodation of Lys-tRNA at the A-site, thus providing structural basis for understanding how the drug and the nascent peptide cooperate to inhibit peptide bond formation and induce translation arrest.

-	~~==About this Structure==~~	+	Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide.,Arenz S, Ramu H, Gupta P, Berninghausen O, Beckmann R, Vazquez-Laslop N, Mankin AS, Wilson DN Nat Commun. 2014 Mar 24;5:3501. doi: 10.1038/ncomms4501. PMID:24662426<ref>PMID:24662426</ref>
-	~~[[3j5l]] is a 33 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli] and [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Streptococcus_sanguinis Streptococcus sanguinis]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024662426</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Streptococcus sanguinis]]		[[Category: Streptococcus sanguinis]]
-	[[Category: Arenz, S.]]	+	[[Category: Arenz, S]]
-	[[Category: Beckmann, R.]]	+	[[Category: Beckmann, R]]
-	[[Category: Berninghausen, O.]]	+	[[Category: Berninghausen, O]]
-	[[Category: Gupta, P.]]	+	[[Category: Gupta, P]]
-	[[Category: Mankin, A S.]]	+	[[Category: Mankin, A S]]
-	[[Category: Ramu, H.]]	+	[[Category: Ramu, H]]
-	[[Category: Vazquez-Laslop, N.]]	+	[[Category: Vazquez-Laslop, N]]
-	[[Category: Wilson, D N.]]	+	[[Category: Wilson, D N]]
	[[Category: Erythromycin]]		[[Category: Erythromycin]]
	[[Category: Ribosome-antibiotic complex]]		[[Category: Ribosome-antibiotic complex]]
	[[Category: Stalling]]		[[Category: Stalling]]

OCA at 06:54, 2 April 2014

OCA — Wed, 02 Apr 2014 06:54:41 GMT

←Older revision		Revision as of 06:54, 2 April 2014
Line 2:		Line 2:
	{{STRUCTURE_3j5l\| PDB=3j5l \| SCENE= }}		{{STRUCTURE_3j5l\| PDB=3j5l \| SCENE= }}
	===Structure of the E. coli 50S subunit with ErmBL nascent chain===		===Structure of the E. coli 50S subunit with ErmBL nascent chain===
		+	{{ABSTRACT_PUBMED_24662426}}

	==Function==		==Function==
Line 10:		Line 11:

	==Reference==		==Reference==
-	<references group="xtra"/><references/>	+	<ref group="xtra">PMID:024662426</ref><references group="xtra"/><references/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Streptococcus sanguinis]]		[[Category: Streptococcus sanguinis]]

OCA at 09:28, 26 March 2014

OCA — Wed, 26 Mar 2014 09:28:36 GMT

←Older revision		Revision as of 09:28, 26 March 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{Large structure}}
		+	{{STRUCTURE_3j5l\| PDB=3j5l \| SCENE= }}
		+	===Structure of the E. coli 50S subunit with ErmBL nascent chain===

-	The ~~entry 3j5l~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL11_ECOLI RL11_ECOLI]] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[http://www.uniprot.org/uniprot/RL13_ECOLI RL13_ECOLI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL4_ECOLI RL4_ECOLI]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.<ref>PMID:2442760</ref> Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).<ref>PMID:2442760</ref> Forms part of the polypeptide exit tunnel.<ref>PMID:2442760</ref> Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.<ref>PMID:2442760</ref> [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL24_ECOLI RL24_ECOLI]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.<ref>PMID:357435</ref> One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.<ref>PMID:357435</ref> [[http://www.uniprot.org/uniprot/RL22_ECOLI RL22_ECOLI]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref>

-	~~Authors~~: ~~Arenz, S~~.~~, Berninghausen, O~~.~~, Beckmann, R~~.~~, Wilson, D~~.N.	+	==About this Structure==
		+	[[3j5l]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Streptococcus_sanguinis Streptococcus sanguinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J5L OCA].

-	~~Description~~: ~~Structure of the E.~~ coli ~~50S subunit with ErmBL nascent chain~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Escherichia coli]]
		+	[[Category: Streptococcus sanguinis]]
		+	[[Category: Arenz, S.]]
		+	[[Category: Beckmann, R.]]
		+	[[Category: Berninghausen, O.]]
		+	[[Category: Gupta, P.]]
		+	[[Category: Mankin, A S.]]
		+	[[Category: Ramu, H.]]
		+	[[Category: Vazquez-Laslop, N.]]
		+	[[Category: Wilson, D N.]]
		+	[[Category: Erythromycin]]
		+	[[Category: Ribosome-antibiotic complex]]
		+	[[Category: Stalling]]

OCA at 07:02, 13 November 2013

OCA — Wed, 13 Nov 2013 07:02:17 GMT

←Older revision		Revision as of 07:02, 13 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3j5l is ON HOLD	+	The entry 3j5l is ON HOLD until Paper Publication

-	Authors: Arenz S, Berninghausen O, Beckmann R, Wilson DN	+	Authors: Arenz, S., Berninghausen, O., Beckmann, R., Wilson, D.N.

	Description: Structure of the E. coli 50S subunit with ErmBL nascent chain		Description: Structure of the E. coli 50S subunit with ErmBL nascent chain