3j37
From Proteopedia
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| - | + | {{Large structure}} | |
| + | {{STRUCTURE_3j37| PDB=3j37 | SCENE= }} | ||
| + | ===Tetracycline resistance protein Tet(O) bound to the ribosome=== | ||
| + | {{ABSTRACT_PUBMED_23403578}} | ||
| - | The | + | ==Function== |
| + | [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI]] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL3_ECOLI RL3_ECOLI]] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL10_ECOLI RL10_ECOLI]] Protein L10 is also a translational repressor protein. It controls the translation of the rplJL-rpoBC operon by binding to its mRNA.[HAMAP-Rule:MF_00362] [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RL1_ECOLI RL1_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] 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_B] [[http://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL31_ECOLI RL31_ECOLI]] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501] [[http://www.uniprot.org/uniprot/RL21_ECOLI RL21_ECOLI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/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/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/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/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/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/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/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/RL23_ECOLI RL23_ECOLI]] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI]] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL17_ECOLI RL17_ECOLI]] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [[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/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL6_ECOLI RL6_ECOLI]] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL14_ECOLI RL14_ECOLI]] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.<ref>PMID:22829778</ref> Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.<ref>PMID:22829778</ref> | ||
| - | + | ==About this Structure== | |
| + | [[3j37]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J37 OCA]. | ||
| - | + | ==Reference== | |
| + | <references group="xtra"/><references/> | ||
| + | [[Category: Escherichia coli]] | ||
| + | [[Category: Allas, U.]] | ||
| + | [[Category: Atkinson, G C.]] | ||
| + | [[Category: Chan, K Y.]] | ||
| + | [[Category: Frank, J.]] | ||
| + | [[Category: Hauryliuk, V.]] | ||
| + | [[Category: Li, W.]] | ||
| + | [[Category: Lu, C.]] | ||
| + | [[Category: Schulten, K.]] | ||
| + | [[Category: Tenson, T.]] | ||
| + | [[Category: Thakor, N S.]] | ||
| + | [[Category: Wilson, K S.]] | ||
| + | [[Category: 70s ribosome]] | ||
| + | [[Category: Antibiotic resistance]] | ||
| + | [[Category: Ribosome]] | ||
Revision as of 01:26, 4 April 2013
Contents |
Tetracycline resistance protein Tet(O) bound to the ribosome
Template:ABSTRACT PUBMED 23403578
Function
[RL9_ECOLI] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [RL2_ECOLI] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [RL3_ECOLI] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [RL16_ECOLI] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [RL10_ECOLI] Protein L10 is also a translational repressor protein. It controls the translation of the rplJL-rpoBC operon by binding to its mRNA.[HAMAP-Rule:MF_00362] [RL25_ECOLI] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [RL1_ECOLI] One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] 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_B] [RL5_ECOLI] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [RL31_ECOLI] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501] [RL21_ECOLI] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [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] [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] [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] [C9QV94_ECOD1] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS020785_004_002551] [RL18_ECOLI] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[1] [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] [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] [RL23_ECOLI] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [RL29_ECOLI] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [RL17_ECOLI] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [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] [RL19_ECOLI] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [RL6_ECOLI] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [RL14_ECOLI] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.[2] Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.[3]
About this Structure
3j37 is a 33 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
- ↑ Newberry V, Brosius J, Garrett R. Fragment of protein L18 from the Escherichia coli ribosome that contains the 5S RNA binding site. Nucleic Acids Res. 1978 Jun;5(6):1753-66. PMID:353728
- ↑ Hauser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P. RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLoS Genet. 2012;8(7):e1002815. doi: 10.1371/journal.pgen.1002815. Epub 2012 Jul , 19. PMID:22829778 doi:10.1371/journal.pgen.1002815
- ↑ Hauser R, Pech M, Kijek J, Yamamoto H, Titz B, Naeve F, Tovchigrechko A, Yamamoto K, Szaflarski W, Takeuchi N, Stellberger T, Diefenbacher ME, Nierhaus KH, Uetz P. RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLoS Genet. 2012;8(7):e1002815. doi: 10.1371/journal.pgen.1002815. Epub 2012 Jul , 19. PMID:22829778 doi:10.1371/journal.pgen.1002815
