5ecw: Difference between revisions
New page: '''Unreleased structure''' The entry 5ecw is ON HOLD Authors: Xu, K., Dedic, E., Brodersen, D.E. Description: Structure of the Shigella flexneri VapC mutant D7A [[Category: Unreleased ... |
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The | ==Structure of the Shigella flexneri VapC mutant D7A== | ||
<StructureSection load='5ecw' size='340' side='right'caption='[[5ecw]], [[Resolution|resolution]] 1.94Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ecw]] 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=5ECW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ECW FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.94Å</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=5ecw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ecw OCA], [https://pdbe.org/5ecw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ecw RCSB], [https://www.ebi.ac.uk/pdbsum/5ecw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ecw ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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;"> | |||
== 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<ref>PMID:26833558</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5ecw" style="background-color:#fffaf0;"></div> | ||
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[[Category: Dedic | ==See Also== | ||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Shigella flexneri]] | |||
[[Category: Brodersen DE]] | |||
[[Category: Dedic E]] | |||
[[Category: Xu K]] | |||
Latest revision as of 09:21, 5 July 2023
Structure of the Shigella flexneri VapC mutant D7AStructure of the Shigella flexneri VapC mutant D7A
Structural highlights
FunctionVAPC_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 PubMedThe 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 AlsoReferences
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