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| | <SX load='2ykr' size='340' side='right' viewer='molstar' caption='[[2ykr]], [[Resolution|resolution]] 9.80Å' scene=''> | | <SX load='2ykr' size='340' side='right' viewer='molstar' caption='[[2ykr]], [[Resolution|resolution]] 9.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ykr]] is a 22 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Escherichia_coli_dh5[alpha] Escherichia coli dh5[alpha]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YKR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YKR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2ykr]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_DH5alpha Escherichia coli DH5alpha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YKR FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vhp|2vhp]]</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]] 9.8Å</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=2ykr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ykr OCA], [http://pdbe.org/2ykr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ykr RCSB], [http://www.ebi.ac.uk/pdbsum/2ykr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ykr ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ykr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ykr OCA], [https://pdbe.org/2ykr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ykr RCSB], [https://www.ebi.ac.uk/pdbsum/2ykr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ykr ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RS11_ECO8A RS11_ECO8A]] 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. [[http://www.uniprot.org/uniprot/E3XT25_ECOLX E3XT25_ECOLX]] 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, probably blocks exit of the E-site tRNA.[HAMAP-Rule:MF_00480] [[http://www.uniprot.org/uniprot/RS17_ECO57 RS17_ECO57]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/E3PE32_ECOH1 E3PE32_ECOH1]] May play a role in 30S ribosomal subunit biogenesis. Unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover.[HAMAP-Rule:MF_01820][SAAS:SAAS00087566] [[http://www.uniprot.org/uniprot/E3PE70_ECOH1 E3PE70_ECOH1]] 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.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/RS13_ECOK1 RS13_ECOK1]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. [[http://www.uniprot.org/uniprot/RS6_ECOSE RS6_ECOSE]] Binds together with S18 to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS3_ECOK1 RS3_ECOK1]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [[http://www.uniprot.org/uniprot/RS12_ECOL6 RS12_ECOL6]] With S4 and S5 plays an important role in translational accuracy. 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 (By similarity). [[http://www.uniprot.org/uniprot/RS14_ECO8A RS14_ECO8A]] 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. [[http://www.uniprot.org/uniprot/B3HGB0_ECOLX B3HGB0_ECOLX]] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] 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.[HAMAP-Rule:MF_01343][RuleBase:RU004524] [[http://www.uniprot.org/uniprot/RS20_ECO55 RS20_ECO55]] Binds directly to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS8_ECOSE RS8_ECOSE]] 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. [[http://www.uniprot.org/uniprot/RS4_ECOK1 RS4_ECOK1]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit (By similarity). With S5 and S12 plays an important role in translational accuracy (By similarity). [[http://www.uniprot.org/uniprot/RS10_ECO24 RS10_ECO24]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RS19_ECOSE RS19_ECOSE]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/D6JG86_ECOLX D6JG86_ECOLX]] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[HAMAP-Rule:MF_01307][SAAS:SAAS00085417] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307][SAAS:SAAS00085429] | + | [https://www.uniprot.org/uniprot/RS2_ECOLI RS2_ECOLI] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: Escherichia coli]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chen, K]] | + | [[Category: Chen K]] |
| - | [[Category: Feng, B]] | + | [[Category: Feng B]] |
| - | [[Category: Gao, N]] | + | [[Category: Gao N]] |
| - | [[Category: Guo, Q]] | + | [[Category: Guo Q]] |
| - | [[Category: Lei, J]] | + | [[Category: Lei J]] |
| - | [[Category: Liu, L]] | + | [[Category: Liu L]] |
| - | [[Category: Xu, Y]] | + | [[Category: Xu Y]] |
| - | [[Category: Yuan, Y]] | + | [[Category: Yuan Y]] |
| - | [[Category: Circularly permutated gtpase]]
| + | |
| - | [[Category: Ribosome biogenesis]]
| + | |
| - | [[Category: Ribosome-hydrolase complex]]
| + | |
| - | [[Category: Yjeq]]
| + | |
| Structural highlights
Function
RS2_ECOLI
Publication Abstract from PubMed
The bacterial RsgA, a circularly permutated GTPase, whose GTPase activity is dependent on the 30S ribosomal subunit, is a late-stage ribosome biogenesis factor involved in the 30S subunit maturation. The role of RsgA is to release another 30S biogenesis factor, RbfA, from the mature 30S subunit in a GTP-dependent manner. Using cryoelectron microscopy, we have determined the structure of the 30S subunit bound with RsgA in the presence of GMPPNP at subnanometer resolution. In the structure, RsgA binds to the central part of the 30S subunit, close to the decoding center, in a position that is incompatible with multiple biogenesis factors, all three translation initiation factors, as well as A-, P-site tRNAs and the 50S subunit. Further structural analysis not only provides a structural model for the RsgA-dependent release of RbfA from the nascent 30S subunit, but also indicates RsgA's role in the ribosomal protein assembly, to promote some tertiary binding protein incorporation. Moreover, together with available biochemical and genetic data, our results suggest that RsgA might be a general checkpoint protein in the late stage of the 30S subunit biogenesis, whose function is not only to release biogenesis factors (e.g., RbfA) from the nascent 30S subunit, but also to block the association of initiation factors to the premature 30S subunit.
Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy.,Guo Q, Yuan Y, Xu Y, Feng B, Liu L, Chen K, Sun M, Yang Z, Lei J, Gao N Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13100-5. Epub 2011 Jul 25. PMID:21788480[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Guo Q, Yuan Y, Xu Y, Feng B, Liu L, Chen K, Sun M, Yang Z, Lei J, Gao N. Structural basis for the function of a small GTPase RsgA on the 30S ribosomal subunit maturation revealed by cryoelectron microscopy. Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13100-5. Epub 2011 Jul 25. PMID:21788480 doi:10.1073/pnas.1104645108
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