5ed0: Difference between revisions

Latest revision as of 06:21, 5 July 2023

Structure of the Shigella flexneri VapC mutant D7N

Structural highlights

5ed0 is a 12 chain structure with sequence from Shigella flexneri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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:https://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:https://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:https://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:https://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:https://dx.doi.org/10.1002/prot.25002

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1111/j.1365-2958.2009.06694.x

[2] 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:https://dx.doi.org/10.1073/pnas.1019587108

[3] 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:https://dx.doi.org/10.1111/j.1365-2958.2009.06694.x

[4] 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:https://dx.doi.org/10.1073/pnas.1019587108

[5] 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:https://dx.doi.org/10.1002/prot.25002

[1]

[2]

[3]

[4]

[5]

@@ Line 3: / Line 3: @@
 <StructureSection load='5ed0' size='340' side='right'caption='[[5ed0]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ed0]] is a 12 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=5ED0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ED0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ed0]] is a 12 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=5ED0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ED0 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ecd|5ecd]]</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]] 2.1&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ed0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ed0 OCA], [https://pdbe.org/5ed0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ed0 RCSB], [https://www.ebi.ac.uk/pdbsum/5ed0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ed0 ProSAT]</span></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=5ed0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ed0 OCA], [http://pdbe.org/5ed0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ed0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ed0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ed0 ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Shigella paradysenteriae weldin 1927]]
 [[Category: Large Structures]]
-[[Category: Brodersen, D E]]
+[[Category: Shigella flexneri]]
-[[Category: Dedic, E]]
+[[Category: Brodersen DE]]
-[[Category: Xu, K]]
+[[Category: Dedic E]]
-[[Category: Hydrolase]]
+[[Category: Xu K]]
-[[Category: Pin-domain]]
-[[Category: Toxin]]

5ed0: Difference between revisions

Latest revision as of 06:21, 5 July 2023

Structure of the Shigella flexneri VapC mutant D7N

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools