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| | ==Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin== | | ==Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin== |
| - | <StructureSection load='5wz4' size='340' side='right' caption='[[5wz4]], [[Resolution|resolution]] 1.77Å' scene=''> | + | <StructureSection load='5wz4' size='340' side='right'caption='[[5wz4]], [[Resolution|resolution]] 1.77Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5wz4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycto Mycto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WZ4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5wz4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WZ4 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wzf|5wzf]]</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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [https://pdbe.org/5wz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [https://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vapC20, Rv2549c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83331 MYCTO])</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=5wz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wz4 OCA], [http://pdbe.org/5wz4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wz4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wz4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wz4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VPC20_MYCTU VPC20_MYCTU]] Toxic component of a type II toxin-antitoxin (TA) system (PubMed:19016878, PubMed:24225902). An endoribonuclease that cleaves both E.coli and M.smegmatis 23S rRNA between G2661 and A2662 in the sarcin-ricin loop (SRL, E.coli 23S rRNA numbering). The SRL sequence is highly conserved and is implicated in GTP hydrolysis by EF-Tu and EF-G. Acts on purified ribosomes but not on isolated RNA in E.coli, nor on a shortened artificial substrate (PubMed:24225902). Upon expression in E.coli inhibits cell growth, colony formation and translation. Its toxic effect is neutralized by coexpression, or subsequent expression (tested over 2 hours) with cognate antitoxin VapB20 (PubMed:19016878, PubMed:24225902).[HAMAP-Rule:MF_00265]<ref>PMID:19016878</ref> <ref>PMID:24225902</ref> | + | [https://www.uniprot.org/uniprot/VPC20_MYCTO VPC20_MYCTO] Toxic component of a toxin-antitoxin (TA) module. An endoribonuclease that cleaves 23S rRNA in the sarcin-ricin loop (SRL). The SRL sequence is highly conserved and is implicated in GTP hydrolysis by EF-Tu and EF-G. Acts on purified ribosomes but not on isolated RNA. Its toxic effect is neutralized by coexpression with cognate antitoxin VapB20.[UniProtKB:P95004][HAMAP-Rule:MF_00265] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5wz4" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5wz4" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Mycto]] | + | [[Category: Large Structures]] |
| - | [[Category: Deep, A]] | + | [[Category: Mycobacterium tuberculosis H37Rv]] |
| - | [[Category: Thakur, K G]] | + | [[Category: Deep A]] |
| - | [[Category: Homodimer]] | + | [[Category: Thakur KG]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Pin-domain]]
| + | |
| - | [[Category: Sarcin-ricin loop cleaving toxin]]
| + | |
| - | [[Category: Toxin-antitoxin system]]
| + | |
| - | [[Category: Vapc toxin]]
| + | |
| Structural highlights
Function
VPC20_MYCTO Toxic component of a toxin-antitoxin (TA) module. An endoribonuclease that cleaves 23S rRNA in the sarcin-ricin loop (SRL). The SRL sequence is highly conserved and is implicated in GTP hydrolysis by EF-Tu and EF-G. Acts on purified ribosomes but not on isolated RNA. Its toxic effect is neutralized by coexpression with cognate antitoxin VapB20.[UniProtKB:P95004][HAMAP-Rule:MF_00265]
Publication Abstract from PubMed
VapBCs, virulence-associated proteins, are the most abundant type II toxin-antitoxin (TA) systems in prokaryotes. Under normal conditions, toxin and antitoxin interact to form a heterooctameric complex, which upon binding to operator sites, inhibits their own expression. Under stress conditions, the VapB antitoxin is degraded by cellular proteases to release a free VapC toxin, which in turn inhibits cell growth mainly by targeting protein translation. However, the intermediate steps involved in the assembly of the heterooctameric complex have not been resolved. Here, we report a 1.75 A resolution crystal structure of VapC20, a Sarcin-Ricin loop cleaving toxin from type II TA system of Mycobacterium tuberculosis. Using analytical ultracentrifugation (AUC) studies, we show that VapC20 exists as a homodimer in solution. The structural analysis of VapC homologs further suggests that VapCs form homodimers. We demonstrate that VapC20 is an obligate homodimer, and its self-association is critical for its folding and activity. Surface plasmon resonance experiments suggest that VapC20 interacts with its cognate antitoxin VapB20 to form a stable complex with nanomolar affinity. A high association rate coupled with a very slow dissociation rate ensures minimal toxicity under normal growth conditions. AUC studies reveal that VapB20 also exists as a homodimer in solution and further associates with VapC20 dimers to form heterotetramers and heterooctamers in a concentration-dependent manner. The results presented here provide valuable insights into the assembly of VapBC family of toxins which is essential for their function and regulation. This article is protected by copyright. All rights reserved.
Crystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin-antitoxin assembly.,Deep A, Kaundal S, Agarwal S, Singh R, Thakur KG FEBS J. 2017 Oct 7. doi: 10.1111/febs.14289. PMID:28986943[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Deep A, Kaundal S, Agarwal S, Singh R, Thakur KG. Crystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin-antitoxin assembly. FEBS J. 2017 Oct 7. doi: 10.1111/febs.14289. PMID:28986943 doi:http://dx.doi.org/10.1111/febs.14289
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