6gc6

Structural highlights

Function

[RL13_ECOLI] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366] [RL20_ECOLI] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [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] [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.^[1] 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.^[2] [RL17_ECOLI] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [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] [RL21_ECOLI] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [RL24_ECOLI] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. It is not thought to be involved in the functions of the mature 50S subunit in vitro.^[3] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.^[4] [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] [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] [RL4_ECOLI] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.^[5] Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).^[6] Forms part of the polypeptide exit tunnel.^[7] Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.^[8] [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] [RL22_ECOLI] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [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] [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]

See Also

• Ribosome 3D structures

References

1. ↑ 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
2. ↑ 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
3. ↑ Spillmann S, Nierhaus KH. The ribosomal protein L24 of Escherichia coli is an assembly protein. J Biol Chem. 1978 Oct 10;253(19):7047-50. PMID:357435
4. ↑ Spillmann S, Nierhaus KH. The ribosomal protein L24 of Escherichia coli is an assembly protein. J Biol Chem. 1978 Oct 10;253(19):7047-50. PMID:357435
5. ↑ Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760
6. ↑ Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760
7. ↑ Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760
8. ↑ Freedman LP, Zengel JM, Archer RH, Lindahl L. Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6516-20. PMID:2442760
9. ↑ Nikolay R, Hilal T, Qin B, Mielke T, Burger J, Loerke J, Textoris-Taube K, Nierhaus KH, Spahn CMT. Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution. Mol Cell. 2018 Jun 7;70(5):881-893.e3. doi: 10.1016/j.molcel.2018.05.003. Epub, 2018 Jun 7. PMID:29883607 doi:http://dx.doi.org/10.1016/j.molcel.2018.05.003