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| | ==Structure of the Shigella flexneri VapC mutant D98N crystal form 1== | | ==Structure of the Shigella flexneri VapC mutant D98N crystal form 1== |
| - | <StructureSection load='5ecd' size='340' side='right' caption='[[5ecd]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='5ecd' size='340' side='right'caption='[[5ecd]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ecd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"shigella_paradysenteriae"_weldin_1927 "shigella paradysenteriae" weldin 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ECD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ECD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ecd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ECD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ECD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vapC, mvpA, stborf2, CP0245 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=623 "Shigella paradysenteriae" Weldin 1927])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></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=5ecd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ecd OCA], [http://pdbe.org/5ecd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ecd RCSB], [http://www.ebi.ac.uk/pdbsum/5ecd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ecd 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=5ecd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ecd OCA], [https://pdbe.org/5ecd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ecd RCSB], [https://www.ebi.ac.uk/pdbsum/5ecd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ecd ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VAPC_SHIFL VAPC_SHIFL]] Toxic component of a toxin-antitoxin (TA) module. A tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits translation, leads to loss of cell growth and degradation of tRNA(fMet); these effects are neutralized by expression of cognate antitoxin VapB. The VapB/VapC complex probably regulates transcription of its own promoter.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref> Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref> | + | [https://www.uniprot.org/uniprot/VAPC_SHIFL VAPC_SHIFL] Toxic component of a toxin-antitoxin (TA) module. A tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits translation, leads to loss of cell growth and degradation of tRNA(fMet); these effects are neutralized by expression of cognate antitoxin VapB. The VapB/VapC complex probably regulates transcription of its own promoter.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref> Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref> |
| | <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 5ecd" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5ecd" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Shigella paradysenteriae weldin 1927]] | + | [[Category: Large Structures]] |
| - | [[Category: Xu, K]] | + | [[Category: Shigella flexneri]] |
| - | [[Category: Hepe]] | + | [[Category: Xu K]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Pin-domain]]
| + | |
| - | [[Category: Toxin]]
| + | |
| Structural highlights
Function
VAPC_SHIFL Toxic component of a toxin-antitoxin (TA) module. A tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits translation, leads to loss of cell growth and degradation of tRNA(fMet); these effects are neutralized by expression of cognate antitoxin VapB. The VapB/VapC complex probably regulates transcription of its own promoter.[1] [2] Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.[3] [4]
Publication Abstract from PubMed
The VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg2+ -dependent ribonuclease and has been shown to target initiator tRNAfMet in vivo. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC appears as a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA/RNA hybrid suggests that the Hepes molecule mimics the position of a target nucleotide. This article is protected by copyright. All rights reserved.
Structural analysis on the active site architecture of the VapC toxin from Shigella flexneri.,Xu K, Dedic E, Brodersen DE Proteins. 2016 Feb 2. doi: 10.1002/prot.25002. PMID:26833558[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Winther KS, Gerdes K. Ectopic production of VapCs from Enterobacteria inhibits translation and trans-activates YoeB mRNA interferase. Mol Microbiol. 2009 May;72(4):918-30. doi: 10.1111/j.1365-2958.2009.06694.x. Epub, 2009 Apr 14. PMID:19400780 doi:http://dx.doi.org/10.1111/j.1365-2958.2009.06694.x
- ↑ Winther KS, Gerdes K. Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7403-7. doi:, 10.1073/pnas.1019587108. Epub 2011 Apr 18. PMID:21502523 doi:http://dx.doi.org/10.1073/pnas.1019587108
- ↑ Winther KS, Gerdes K. Ectopic production of VapCs from Enterobacteria inhibits translation and trans-activates YoeB mRNA interferase. Mol Microbiol. 2009 May;72(4):918-30. doi: 10.1111/j.1365-2958.2009.06694.x. Epub, 2009 Apr 14. PMID:19400780 doi:http://dx.doi.org/10.1111/j.1365-2958.2009.06694.x
- ↑ Winther KS, Gerdes K. Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7403-7. doi:, 10.1073/pnas.1019587108. Epub 2011 Apr 18. PMID:21502523 doi:http://dx.doi.org/10.1073/pnas.1019587108
- ↑ Xu K, Dedic E, Brodersen DE. Structural analysis on the active site architecture of the VapC toxin from Shigella flexneri. Proteins. 2016 Feb 2. doi: 10.1002/prot.25002. PMID:26833558 doi:http://dx.doi.org/10.1002/prot.25002
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