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| | <StructureSection load='6ifc' size='340' side='right'caption='[[6ifc]], [[Resolution|resolution]] 1.99Å' scene=''> | | <StructureSection load='6ifc' size='340' side='right'caption='[[6ifc]], [[Resolution|resolution]] 1.99Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ifc]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IFC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ifc]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IFC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.99Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vapC, STM3033 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY]), vapB, STM3034 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6ifc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ifc OCA], [http://pdbe.org/6ifc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ifc RCSB], [http://www.ebi.ac.uk/pdbsum/6ifc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ifc 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=6ifc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ifc OCA], [https://pdbe.org/6ifc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ifc RCSB], [https://www.ebi.ac.uk/pdbsum/6ifc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ifc ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VAPC_SALTY VAPC_SALTY]] Toxic component of a type II toxin-antitoxin (TA) system. A site-specific 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. Expression also activates translation initiation at correctly positioned elongator codons (AAA and to a lesser extent AAG). Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity. [[http://www.uniprot.org/uniprot/VAPB_SALTY VAPB_SALTY]] Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli neutralizes the effect of cognate toxin VapC.<ref>PMID:19400780</ref> <ref>PMID:21502523</ref> | + | [https://www.uniprot.org/uniprot/VAPB_SALTY VAPB_SALTY] Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli neutralizes the effect of cognate toxin VapC.<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 6ifc" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6ifc" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Salty]] | + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]] |
| - | [[Category: Lee, B J]] | + | [[Category: Lee BJ]] |
| - | [[Category: Park, D W]] | + | [[Category: Park DW]] |
| - | [[Category: Toxin-antitoxin]]
| + | |
| - | [[Category: Toxin-antitoxin complex]]
| + | |
| Structural highlights
Function
VAPB_SALTY Antitoxin component of a type II toxin-antitoxin (TA) system. Upon expression in E.coli neutralizes the effect of cognate toxin VapC.[1] [2]
Publication Abstract from PubMed
Bacterial toxin-antitoxin (TA) system has gained attention for its essential roles in cellular maintenance and survival under harsh environmental conditions such as nutrient deficiency and antibiotic treatment. There are at least 14 TA systems in Salmonella enterica serovar Typhimurium LT2, a pathogenic bacterium, and none of the structures of these TA systems have been determined. We determined the crystal structure of the VapBC TA complex from S. Typhimurium LT2 in proteolyzed and DNA-bound forms at 2.0 A and 2.8 A resolution, respectively. The VapC toxin possesses a pilT N-terminal domain (PIN-domain) that shows ribonuclease activity, and the VapB antitoxin has an AbrB-type DNA binding domain. In addition, the structure revealed details of interaction mode between VapBC and the cognate promoter DNA, including the inhibition of VapC by VapB and linear conformation of bound DNA in the VapBC complex. The complexation of VapBC with the linear DNA is not consistent with known structures of VapBC homologs in complex with bent DNA. We also identified VapC from S. Typhimurium LT2 as a putative Ca(2+) -dependent ribonuclease, which differs from previous data showing that VapC homologs have Mg(2+) or Mn(2+) -dependent ribonuclease activities. The present studies could provide structural understanding of the physiology of VapBC systems and foundation for the development of new antibiotic drugs against Salmonella infection.
Crystal structure of proteolyzed VapBC and DNA-bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca(2+) -dependent ribonuclease.,Park D, Yoon HJ, Lee KY, Park SJ, Cheon SH, Lee HH, Lee SJ, Lee BJ FASEB J. 2019 Dec 23. doi: 10.1096/fj.201901989R. PMID:31908032[3]
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
- ↑ Park D, Yoon HJ, Lee KY, Park SJ, Cheon SH, Lee HH, Lee SJ, Lee BJ. Crystal structure of proteolyzed VapBC and DNA-bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca(2+) -dependent ribonuclease. FASEB J. 2019 Dec 23. doi: 10.1096/fj.201901989R. PMID:31908032 doi:http://dx.doi.org/10.1096/fj.201901989R
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