5uz4

Structural highlights

Function

[RS12_ECO45] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_00403] [RSGA_ECOLI] One of at least 4 proteins (Era, RbfA, RimM and RsgA/YjeQ) that assist in the late maturation steps of the functional core of the 30S ribosomal subunit (PubMed:18223068, PubMed:21102555, PubMed:21303937, PubMed:25904134, PubMed:27382067). Binds the 30S subunit contacting the head, platform, and rRNA helix 44, which may assist the last maturation stages (PubMed:21788480, PubMed:21960487). Removes RbfA from mature, but not immature 30S ribosomes in a GTP-dependent manner; 95% removal in the presence of GTP, 90% removal in GMP-PNP and 65% removal in the presence of GDP (PubMed:21102555, PubMed:25904134). Circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover (PubMed:12220175). Dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96-fold increase in kcat) ribosomes (PubMed:14973029). Mature 30S ribosomes stimulate intrinsic GTPase more than do immature 30S ribosomes (PubMed:25904134). Ribosome-associated GTPase activity is stimulated by RbfA (PubMed:21102555). The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin (PubMed:15466596) streptomycin and spectinomycin (PubMed:15828870). This inhibition is not due to competition for binding sites on the 30S or 70S ribosome (PubMed:15828870).^{[1] [2] [3] [4] [5] [6] [7] [8]} [RS8_ECO45] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. [RS3_ECO45] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [RS18_ECO45] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit. [RS19_ECO45] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [RS14_ECO45] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site. [RS17_ECO45] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [RS7_ECOLI] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, where it has been shown to contact mRNA. Has been shown to contact tRNA in both the P and E sites; it probably blocks exit of the E site tRNA.^[9] Protein S7 is also a translational repressor protein; it regulates the expression of the str operon members to different degrees by binding to its mRNA.^[10] [RS4_ECO45] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. [RS10_ECO45] Involved in the binding of tRNA to the ribosomes. [RS13_ECO57] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the E.coli 70S ribosome in the initiation state it has been modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change. Contacts the tRNAs in the A and P sites (By similarity). [RS15_ECO57] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [RS5_ECO57] With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. [RS11_ECO45] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. [RS20_ECO45] Binds directly to 16S ribosomal RNA. [RS6_ECOLI] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360]

See Also

• Ribosome 3D structures

References

1. ↑ Daigle DM, Rossi L, Berghuis AM, Aravind L, Koonin EV, Brown ED. YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics. Biochemistry. 2002 Sep 17;41(37):11109-17. PMID:12220175
2. ↑ Daigle DM, Brown ED. Studies of the interaction of Escherichia coli YjeQ with the ribosome in vitro. J Bacteriol. 2004 Mar;186(5):1381-7. PMID:14973029
3. ↑ Himeno H, Hanawa-Suetsugu K, Kimura T, Takagi K, Sugiyama W, Shirata S, Mikami T, Odagiri F, Osanai Y, Watanabe D, Goto S, Kalachnyuk L, Ushida C, Muto A. A novel GTPase activated by the small subunit of ribosome. Nucleic Acids Res. 2004 Oct 5;32(17):5303-9. Print 2004. PMID:15466596 doi:http://dx.doi.org/10.1093/nar/gkh861
4. ↑ Campbell TL, Daigle DM, Brown ED. Characterization of the Bacillus subtilis GTPase YloQ and its role in ribosome function. Biochem J. 2005 Aug 1;389(Pt 3):843-52. PMID:15828870 doi:http://dx.doi.org/BJ20041873
5. ↑ Goto S, Kato S, Kimura T, Muto A, Himeno H. RsgA releases RbfA from 30S ribosome during a late stage of ribosome biosynthesis. EMBO J. 2011 Jan 5;30(1):104-14. doi: 10.1038/emboj.2010.291. Epub 2010 Nov 23. PMID:21102555 doi:http://dx.doi.org/10.1038/emboj.2010.291
6. ↑ Jeganathan A, Razi A, Thurlow B, Ortega J. The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly. RNA. 2015 Jun;21(6):1203-16. doi: 10.1261/rna.049171.114. Epub 2015 Apr 22. PMID:25904134 doi:http://dx.doi.org/10.1261/rna.049171.114
7. ↑ Campbell TL, Brown ED. Genetic interaction screens with ordered overexpression and deletion clone sets implicate the Escherichia coli GTPase YjeQ in late ribosome biogenesis. J Bacteriol. 2008 Apr;190(7):2537-45. Epub 2008 Jan 25. PMID:18223068 doi:http://dx.doi.org/JB.01744-07
8. ↑ Thurlow B, Davis JH, Leong V, F Moraes T, Williamson JR, Ortega J. Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit. Nucleic Acids Res. 2016 Nov 16;44(20):9918-9932. Epub 2016 Jul 5. PMID:27382067 doi:http://dx.doi.org/10.1093/nar/gkw613
9. ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
10. ↑ Nowotny V, Nierhaus KH. Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7. Biochemistry. 1988 Sep 6;27(18):7051-5. PMID:2461734
11. ↑ Razi A, Guarne A, Ortega J. The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly. Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):E3396-E3403. doi:, 10.1073/pnas.1618016114. Epub 2017 Apr 10. PMID:28396444 doi:http://dx.doi.org/10.1073/pnas.1618016114