3j8g - Revision history

OCA at 08:40, 7 February 2024

OCA — Wed, 07 Feb 2024 08:40:36 GMT

←Older revision		Revision as of 08:40, 7 February 2024
Line 3:		Line 3:
	<SX load='3j8g' size='340' side='right' viewer='molstar' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>		<SX load='3j8g' size='340' side='right' viewer='molstar' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli] and [https://en.wikipedia.org/wiki/Escherichia_coli_k12~~ Escherichia coli ~~k12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j8g]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J8G FirstGlance]. <br>
-	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [https://pdbe.org/3j8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [https://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></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]] 5Å</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [https://pdbe.org/3j8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [https://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~C9QXP2_ECOD1 C9QXP2_ECOD1]~~] 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 (By similarity).[HAMAP-Rule:MF_01366] [[https://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA ~~and is necessary for the in vitro assembly process of the 50S ribosomal subunit~~. ~~It is not involved in~~ the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[https://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[https://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[https://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[https://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[https://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is ~~quite~~ mobile in the ribosome, ~~and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to~~ its mRNA.[HAMAP-Rule:MF_01318] [[https://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[https://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[https://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[https://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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~~] [[https://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[https://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[https://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[https://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[https://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[https://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[https://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[https://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[https://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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/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]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, and intriguingly, it contains two consecutive GTPase domains (GD), being one-of-a-kind among all known GTPases. EngA is required for the 50S subunit maturation. However, its molecular role remains elusive. Here, we present the structure of EngA bound to the 50S subunit. Our data show that EngA binds to the peptidyl transferase center (PTC) and induces dramatic conformational changes on the 50S subunit, which virtually returns the 50S subunit to a state similar to that of the late-stage 50S assembly intermediates. Very interestingly, our data show that the two GDs exhibit a pseudo-two-fold symmetry in the 50S-bound conformation. Our results indicate that EngA recognizes certain forms of the 50S assembly intermediates, and likely facilitates the conformational maturation of the PTC of the 23S rRNA in a direct manner. Furthermore, in a broad context, our data also suggest that EngA might be a sensor of the cellular GTP/GDP ratio, endowed with multiple conformational states, in response to fluctuations in cellular nucleotide pool, to facilitate and regulate ribosome assembly.	+
-		+
-	Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly.,Zhang X, Yan K, Zhang Y, Li N, Ma C, Li Z, Zhang Y, Feng B, Liu J, Sun Y, Xu Y, Lei J, Gao N Nucleic Acids Res. 2014 Nov 11. pii: gku1135. PMID:25389271<ref>PMID:25389271</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3j8g" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</SX>		</SX>
-	~~[[Category: Ecoli]]~~	+	[[Category: Escherichia coli K-12]]
-	[[Category: Escherichia coli ~~k12~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Feng, B]]	+	[[Category: Feng B]]
-	[[Category: Gao, N]]	+	[[Category: Gao N]]
-	[[Category: Lei, J]]	+	[[Category: Lei J]]
-	[[Category: Li, N]]	+	[[Category: Li N]]
-	[[Category: Li, Z]]	+	[[Category: Li Z]]
-	[[Category: Liu, J]]	+	[[Category: Liu J]]
-	[[Category: Ma, C]]	+	[[Category: Ma C]]
-	[[Category: Sun, Y]]	+	[[Category: Sun Y]]
-	[[Category: Xu, Y]]	+	[[Category: Xu Y]]
-	[[Category: Yan, K]]	+	[[Category: Yan K]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang X]]
-	[[Category: Zhang, Y]]	+	[[Category: Zhang Y]]
-	~~[[Category: Der]]~~	+
-	~~[[Category: Enga]]~~	+
-	~~[[Category: Gtpase]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Ribosome assembly]]~~	+
-	~~[[Category: Rna folding]]~~	+
-	~~[[Category: Yphc~~]]	+

OCA at 13:28, 4 May 2022

OCA — Wed, 04 May 2022 13:28:05 GMT

←Older revision		Revision as of 13:28, 4 May 2022
Line 3:		Line 3:
	<SX load='3j8g' size='340' side='right' viewer='molstar' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>		<SX load='3j8g' size='340' side='right' viewer='molstar' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli] and [~~http~~://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3J8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli] and [https://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J8G FirstGlance]. <br>
-	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [~~http~~://pdbe.org/3j8g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>	+	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [https://pdbe.org/3j8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [https://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[~~http~~://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[~~http~~://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[~~http~~://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[~~http~~://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[~~http~~://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[~~http~~://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[~~http~~://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[~~http~~://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[~~http~~://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[~~http~~://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[~~http~~://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[~~http~~://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[~~http~~://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[~~http~~://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[~~http~~://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[~~http~~://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[~~http~~://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[~~http~~://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[~~http~~://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[~~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]	+	[[https://www.uniprot.org/uniprot/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[https://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[https://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[https://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[https://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[https://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[https://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[https://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[https://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[https://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[https://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[https://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[https://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[https://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[https://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[https://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[https://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[https://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[https://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[https://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:09, 10 April 2020

OCA — Fri, 10 Apr 2020 18:09:23 GMT

←Older revision		Revision as of 18:09, 10 April 2020
Line 3:		Line 3:
	<SX load='3j8g' size='340' side='right' viewer='molstar' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>		<SX load='3j8g' size='340' side='right' viewer='molstar' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3J8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J8G FirstGlance]. <br>
-	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://pdbe.org/3j8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>	+	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://pdbe.org/3j8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 17:30, 6 March 2020

OCA — Fri, 06 Mar 2020 17:30:00 GMT

←Older revision		Revision as of 17:30, 6 March 2020
Line 1:		Line 1:

	==Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit==		==Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit==
-	<~~StructureSection~~ load='3j8g' size='340' side='right'caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>	+	<SX load='3j8g' size='340' side='right' viewer='molstar' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>
Line 7:		Line 7:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/~~C9QXH2_ECOD1 C9QXH2_ECOD1~~]] ~~Binds to~~ 23S rRNA. ~~Forms part~~ of ~~two intersubunit bridges~~ in the ~~70S~~ ribosome.[HAMAP-Rule:~~MF_01367][RuleBase:RU003950~~] [[http://www.uniprot.org/uniprot/~~C9QPR2_ECOD1 C9QPR2_ECOD1~~]] ~~GTPase that plays an essential role~~ in the ~~late steps of~~ ribosome ~~biogenesis~~.[HAMAP-Rule:~~MF_00195~~][RuleBase:~~RU004481~~] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Ecoli]]		[[Category: Ecoli]]
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]

OCA at 08:10, 18 December 2019

OCA — Wed, 18 Dec 2019 08:10:49 GMT

←Older revision		Revision as of 08:10, 18 December 2019
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit==		==Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit==
-	<StructureSection load='3j8g' size='340' side='right' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>	+	<StructureSection load='3j8g' size='340' side='right'caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>
	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://pdbe.org/3j8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>		</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://pdbe.org/3j8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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]
Line 24:		Line 23:
	[[Category: Ecoli]]		[[Category: Ecoli]]
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
		+	[[Category: Large Structures]]
	[[Category: Feng, B]]		[[Category: Feng, B]]
	[[Category: Gao, N]]		[[Category: Gao, N]]

OCA at 09:30, 19 December 2018

OCA — Wed, 19 Dec 2018 09:30:17 GMT

←Older revision		Revision as of 09:30, 19 December 2018
Line 3:		Line 3:
	<StructureSection load='3j8g' size='340' side='right' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>		<StructureSection load='3j8g' size='340' side='right' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>
	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://pdbe.org/3j8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>		</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://pdbe.org/3j8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>
	</table>		</table>
	{{Large structure}}		{{Large structure}}
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/~~C9QXG3_ECOD1 C9QXG3_ECOD1~~]] ~~Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 ~~(By similarity)~~.[HAMAP-Rule:~~MF_01328~~] [[http://www.uniprot.org/uniprot/~~C9QXH2_ECOD1 C9QXH2_ECOD1~~]] ~~Binds to 23S rRNA. Forms part of two intersubunit bridges~~ in the ~~70S~~ ribosome.[HAMAP-Rule:~~MF_01367~~][RuleBase:~~RU003950~~] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559~~] [[http://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481~~] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
	[[Category: Feng, B]]		[[Category: Feng, B]]

OCA at 10:49, 5 August 2016

OCA — Fri, 05 Aug 2016 10:49:55 GMT

←Older revision		Revision as of 10:49, 5 August 2016
Line 1:		Line 1:
		+	{{Large structure}}
	==Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit==		==Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit==
	<StructureSection load='3j8g' size='340' side='right' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>		<StructureSection load='3j8g' size='340' side='right' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>
-	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum]</span></td></tr>	+	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://pdbe.org/3j8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j8g ProSAT]</span></td></tr>
	</table>		</table>
		+	{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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]
Line 15:		Line 17:
	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 3j8g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:45, 25 December 2014

OCA — Thu, 25 Dec 2014 01:45:39 GMT

←Older revision		Revision as of 01:45, 25 December 2014
Line 5:		Line 5:
	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum]</span></td></tr>		</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/C9QXP2_ECOD1 C9QXP2_ECOD1]] 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 (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/C9QTZ1_ECOD1 C9QTZ1_ECOD1]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[RuleBase:RU000560][HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/C9QXG9_ECOD1 C9QXG9_ECOD1]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/C9QXH3_ECOD1 C9QXH3_ECOD1]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[HAMAP-Rule:MF_01326] 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 (By similarity).[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C9QRC1_ECOD1 C9QRC1_ECOD1]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS00023223] [[http://www.uniprot.org/uniprot/C9QTM2_ECOD1 C9QTM2_ECOD1]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/H0QFK1_ECOLI H0QFK1_ECOLI]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318] [[http://www.uniprot.org/uniprot/C9QXG7_ECOD1 C9QXG7_ECOD1]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity).[HAMAP-Rule:MF_01331] 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 (By similarity).[RuleBase:RU004008][HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/C9QXH7_ECOD1 C9QXH7_ECOD1]] This protein binds to the 23S rRNA, and 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/C9QXG5_ECOD1 C9QXG5_ECOD1]] One of the primary rRNA binding proteins. 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 somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C9QXH4_ECOD1 C9QXH4_ECOD1]] 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. 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] [[http://www.uniprot.org/uniprot/C9QXH8_ECOD1 C9QXH8_ECOD1]] This is one 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/C9QY61_ECOD1 C9QY61_ECOD1]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C9QXG2_ECOD1 C9QXG2_ECOD1]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325] [[http://www.uniprot.org/uniprot/B1X6G9_ECODH B1X6G9_ECODH]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/C9QXG3_ECOD1 C9QXG3_ECOD1]] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328] 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 (By similarity).[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C9QXH2_ECOD1 C9QXH2_ECOD1]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/C9R119_ECOD1 C9R119_ECOD1]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C9QPR2_ECOD1 C9QPR2_ECOD1]] GTPase that plays an essential role in the late steps of ribosome biogenesis.[HAMAP-Rule:MF_00195][RuleBase:RU004481] [[http://www.uniprot.org/uniprot/C9QV94_ECOD1 C9QV94_ECOD1]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [[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]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 08:02, 26 November 2014

OCA — Wed, 26 Nov 2014 08:02:40 GMT

←Older revision		Revision as of 08:02, 26 November 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit==
		+	<StructureSection load='3j8g' size='340' side='right' caption='[[3j8g]], [[Resolution\|resolution]] 5.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3j8g]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J8G FirstGlance]. <br>
		+	</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=3j8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j8g RCSB], [http://www.ebi.ac.uk/pdbsum/3j8g PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, and intriguingly, it contains two consecutive GTPase domains (GD), being one-of-a-kind among all known GTPases. EngA is required for the 50S subunit maturation. However, its molecular role remains elusive. Here, we present the structure of EngA bound to the 50S subunit. Our data show that EngA binds to the peptidyl transferase center (PTC) and induces dramatic conformational changes on the 50S subunit, which virtually returns the 50S subunit to a state similar to that of the late-stage 50S assembly intermediates. Very interestingly, our data show that the two GDs exhibit a pseudo-two-fold symmetry in the 50S-bound conformation. Our results indicate that EngA recognizes certain forms of the 50S assembly intermediates, and likely facilitates the conformational maturation of the PTC of the 23S rRNA in a direct manner. Furthermore, in a broad context, our data also suggest that EngA might be a sensor of the cellular GTP/GDP ratio, endowed with multiple conformational states, in response to fluctuations in cellular nucleotide pool, to facilitate and regulate ribosome assembly.

-	~~The entry 3j8g is ON HOLD~~	+	Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly.,Zhang X, Yan K, Zhang Y, Li N, Ma C, Li Z, Zhang Y, Feng B, Liu J, Sun Y, Xu Y, Lei J, Gao N Nucleic Acids Res. 2014 Nov 11. pii: gku1135. PMID:25389271<ref>PMID:25389271</ref>

-	~~Authors: Zhang~~, X.~~, Yan, K~~.~~, Zhang, Y~~., Li, N., ~~Ma, C.~~, Li, Z~~., Zhang, Y., Feng, B.,~~ Liu, J., Sun, Y., Xu, Y., ~~Lei~~, J., ~~Gao, N.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli k12]]
		+	[[Category: Feng, B]]
		+	[[Category: Gao, N]]
		+	[[Category: Lei, J]]
		+	[[Category: Li, N]]
		+	[[Category: Li, Z]]
		+	[[Category: Liu, J]]
		+	[[Category: Ma, C]]
		+	[[Category: Sun, Y]]
		+	[[Category: Xu, Y]]
		+	[[Category: Yan, K]]
		+	[[Category: Zhang, X]]
		+	[[Category: Zhang, Y]]
		+	[[Category: Der]]
		+	[[Category: Enga]]
		+	[[Category: Gtpase]]
		+	[[Category: Ribosome]]
		+	[[Category: Ribosome assembly]]
		+	[[Category: Rna folding]]
		+	[[Category: Yphc]]

OCA at 11:01, 19 November 2014

OCA — Wed, 19 Nov 2014 11:01:00 GMT

←Older revision		Revision as of 11:01, 19 November 2014
Line 3:		Line 3:
	The entry 3j8g is ON HOLD		The entry 3j8g is ON HOLD

-	Authors: ~~Xiaoxiao Z~~, ~~Kaige~~ Y, ~~Yixiao Z~~, ~~Ningning L~~, ~~Chengying M~~, ~~Zhifei L~~, ~~Yanqing~~ Z, ~~Boya F~~, ~~Jing L~~, ~~Yadong S~~, ~~Yanji X~~, ~~Jianlin L~~, ~~Ning G~~	+	Authors: Zhang, X., Yan, K., Zhang, Y., Li, N., Ma, C., Li, Z., Zhang, Y., Feng, B., Liu, J., Sun, Y., Xu, Y., Lei, J., Gao, N.

	Description: Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit		Description: Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit