|
|
| (2 intermediate revisions not shown.) |
| Line 3: |
Line 3: |
| | <SX load='6pvk' size='340' side='right' viewer='molstar' caption='[[6pvk]], [[Resolution|resolution]] 3.40Å' scene=''> | | <SX load='6pvk' size='340' side='right' viewer='molstar' caption='[[6pvk]], [[Resolution|resolution]] 3.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6pvk]] is a 17 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PVK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6pvk]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PVK FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6ppf|6ppf]], [[6ppk|6ppk]]</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]] 3.4Å</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=6pvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pvk OCA], [http://pdbe.org/6pvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pvk RCSB], [http://www.ebi.ac.uk/pdbsum/6pvk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pvk 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=6pvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pvk OCA], [https://pdbe.org/6pvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pvk RCSB], [https://www.ebi.ac.uk/pdbsum/6pvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pvk ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A063X754_BACIU A0A063X754_BACIU]] 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/A0A063XIS2_BACIU A0A063XIS2_BACIU]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00352917] [[http://www.uniprot.org/uniprot/A0A063X745_BACIU A0A063X745_BACIU]] 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][RuleBase:RU003906] [[http://www.uniprot.org/uniprot/A0A063XCP1_BACIU A0A063XCP1_BACIU]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00124822] [[http://www.uniprot.org/uniprot/A0A063XHU6_BACIU A0A063XHU6_BACIU]] 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/A0A063XCB6_BACIU A0A063XCB6_BACIU]] 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/F5HRT3_BACIU F5HRT3_BACIU]] 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.[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.[HAMAP-Rule:MF_01331][RuleBase:RU004008] [[http://www.uniprot.org/uniprot/F5HRS7_BACIU F5HRS7_BACIU]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[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.[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/A0A063X8U6_BACIU A0A063X8U6_BACIU]] Forms part of the polypeptide exit tunnel.[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.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/A0A063XFC1_BACIU A0A063XFC1_BACIU]] 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.[HAMAP-Rule:MF_00382][RuleBase:RU000560] [[http://www.uniprot.org/uniprot/A0A063XB36_BACIU A0A063XB36_BACIU]] 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/A0A063XCH0_BACIU A0A063XCH0_BACIU]] 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][RuleBase:RU003878][SAAS:SAAS00725369] | + | [https://www.uniprot.org/uniprot/RL2_BACSU RL2_BACSU] 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 (By similarity).[HAMAP-Rule:MF_01320] |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most bacteria. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome. We present here the cryo-electron microscopy structure of RbgA bound to a Bacillus subtilis 50S subunit assembly intermediate (45SRbgA particle) that accumulates in cells upon RbgA depletion. Binding of RbgA at the P site of the immature particle stabilizes functionally important rRNA helices in the A and P-sites, prior to the completion of the maturation process of the subunit. The structure also reveals the location of the highly conserved N-terminal end of RbgA containing the catalytic residue Histidine 9. The derived model supports a mechanism of GTP hydrolysis, and it shows that upon interaction of RbgA with the 45SRbgA particle, Histidine 9 positions itself near the nucleotide potentially acting as the catalytic residue with minimal rearrangements. This structure represents the first visualization of the conformational changes induced by an assembly factor in a bacterial subunit intermediate. |
| | + | |
| | + | Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.,Seffouh A, Jain N, Jahagirdar D, Basu K, Razi A, Ni X, Guarne A, Britton RA, Ortega J Nucleic Acids Res. 2019 Nov 4;47(19):10414-10425. doi: 10.1093/nar/gkz770. PMID:31665744<ref>PMID:31665744</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 6pvk" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Ribosome 3D structures|Ribosome 3D structures]] | | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| | [[Category: Bacillus subtilis]] | | [[Category: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Basu, K]] | + | [[Category: Basu K]] |
| - | [[Category: Britton, R A]] | + | [[Category: Britton RA]] |
| - | [[Category: Guarne, A]] | + | [[Category: Guarne A]] |
| - | [[Category: Jahagirdar, D]] | + | [[Category: Jahagirdar D]] |
| - | [[Category: Jain, N]] | + | [[Category: Jain N]] |
| - | [[Category: Ni, X]] | + | [[Category: Ni X]] |
| - | [[Category: Ortega, J]] | + | [[Category: Ortega J]] |
| - | [[Category: Razi, A]] | + | [[Category: Razi A]] |
| - | [[Category: Seffouh, A]] | + | [[Category: Seffouh A]] |
| - | [[Category: 50s subunit]]
| + | |
| - | [[Category: Rbga]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Ribosome assembly]]
| + | |
| - | [[Category: Ylqf]]
| + | |
| Structural highlights
Function
RL2_BACSU 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 (By similarity).[HAMAP-Rule:MF_01320]
Publication Abstract from PubMed
Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most bacteria. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome. We present here the cryo-electron microscopy structure of RbgA bound to a Bacillus subtilis 50S subunit assembly intermediate (45SRbgA particle) that accumulates in cells upon RbgA depletion. Binding of RbgA at the P site of the immature particle stabilizes functionally important rRNA helices in the A and P-sites, prior to the completion of the maturation process of the subunit. The structure also reveals the location of the highly conserved N-terminal end of RbgA containing the catalytic residue Histidine 9. The derived model supports a mechanism of GTP hydrolysis, and it shows that upon interaction of RbgA with the 45SRbgA particle, Histidine 9 positions itself near the nucleotide potentially acting as the catalytic residue with minimal rearrangements. This structure represents the first visualization of the conformational changes induced by an assembly factor in a bacterial subunit intermediate.
Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.,Seffouh A, Jain N, Jahagirdar D, Basu K, Razi A, Ni X, Guarne A, Britton RA, Ortega J Nucleic Acids Res. 2019 Nov 4;47(19):10414-10425. doi: 10.1093/nar/gkz770. PMID:31665744[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Seffouh A, Jain N, Jahagirdar D, Basu K, Razi A, Ni X, Guarné A, Britton RA, Ortega J. Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate. Nucleic Acids Res. 2019 Nov 4;47(19):10414-10425. PMID:31665744 doi:10.1093/nar/gkz770
|
