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<StructureSection load='3dbo' size='340' side='right'caption='[[3dbo]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
<StructureSection load='3dbo' size='340' side='right'caption='[[3dbo]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3dbo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DBO FirstGlance]. <br>
<table><tr><td colspan='2'>[[3dbo]] 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=3DBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DBO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.76&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rv0626, MT0654 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), Rv0627 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=3dbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbo OCA], [https://pdbe.org/3dbo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dbo RCSB], [https://www.ebi.ac.uk/pdbsum/3dbo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbo ProSAT], [https://www.topsan.org/Proteins/ISFI/3dbo TOPSAN]</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=3dbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbo OCA], [https://pdbe.org/3dbo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dbo RCSB], [https://www.ebi.ac.uk/pdbsum/3dbo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbo ProSAT], [https://www.topsan.org/Proteins/ISFI/3dbo TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/VAPB5_MYCTO VAPB5_MYCTO]] Probable antitoxin component of a probable toxin-antitoxin (TA) module. The cognate toxin is VapC5 (By similarity). [[https://www.uniprot.org/uniprot/VAPC5_MYCTU VAPC5_MYCTU]] Probable toxic component of a type II toxin-antitoxin (TA) module. The cognate antitoxin is VapB5. Has limited RNase activity on substrates; activity is seen with a VapC5-VapB5 complex.<ref>PMID:18952600</ref>
[https://www.uniprot.org/uniprot/VAPB5_MYCTU VAPB5_MYCTU] Probable antitoxin component of a type II toxin-antitoxin (TA) system. The cognate toxin is VapC5.<ref>PMID:18952600</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dbo ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3dbo ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In prokaryotes, cognate toxin-antitoxin pairs have long been known, but no three-dimensional structure has been available for any given complex from Mycobacterium tuberculosis. Here we report the crystal structure and activity of a member of the VapBC family of complexes from M. tuberculosis. The toxin VapC-5 is a compact, 150 residues, two domain alpha/beta protein. Bent around the toxin is the VapB-5 antitoxin, a 33-residue alpha-helix. Assays suggest that the toxin is an Mg-enabled endoribonuclease, inhibited by the antitoxin. The lack of DNase activity is consistent with earlier suggestions that the complex represses its own operon. Furthermore, analysis of the interactions in the binding of the antitoxin to the toxin suggest that exquisite control is required to protect the bacteria cell from toxic VapC-5.
Structure and proposed activity of a member of the VapBC family of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis.,Miallau L, Faller M, Chiang J, Arbing M, Guo F, Cascio D, Eisenberg D J Biol Chem. 2009 Jan 2;284(1):276-83. Epub 2008 Oct 24. PMID:18952600<ref>PMID:18952600</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3dbo" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Myctu]]
[[Category: Mycobacterium tuberculosis H37Rv]]
[[Category: Cascio, D]]
[[Category: Cascio D]]
[[Category: Eisenberg, D]]
[[Category: Eisenberg D]]
[[Category: ISFI, Integrated Center for Structure and Function Innovation]]
[[Category: Miallau L]]
[[Category: Miallau, L]]
[[Category: Structural genomic]]
[[Category: Integrated center for structure and function innovation]]
[[Category: Isfi]]
[[Category: Mycobacterium tuberculosis]]
[[Category: PSI, Protein structure initiative]]
[[Category: Tbsgc]]
[[Category: Toxin antitoxin complex]]
[[Category: Toxin-antitoxin complex]]
[[Category: Vapbc]]

Latest revision as of 09:40, 21 February 2024

Crystal structure of a member of the VapBC family of toxin-antitoxin systems, VapBC-5, from Mycobacterium tuberculosis

3dbo, resolution 1.76Å

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