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5xko

From Proteopedia

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Current revision (10:19, 27 March 2024) (edit) (undo)
 
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<StructureSection load='5xko' size='340' side='right'caption='[[5xko]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
<StructureSection load='5xko' size='340' side='right'caption='[[5xko]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5xko]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XKO FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5xko]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XKO FirstGlance]. <br>
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</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=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xkp|5xkp]], [[5xkq|5xkq]], [[5xkr|5xkr]]</td></tr>
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<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=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xko OCA], [http://pdbe.org/5xko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xko RCSB], [http://www.ebi.ac.uk/pdbsum/5xko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xko ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5xko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xko OCA], [https://pdbe.org/5xko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xko RCSB], [https://www.ebi.ac.uk/pdbsum/5xko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xko ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0QY90_MYCS2 A0QY90_MYCS2]
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Structure-based methods are powerful tools that are being exploited to unravel new functions with therapeutic advantage. Here, we report the discovery of a new class of deaminases, predominantly found in mycobacterial species that act on the commercially important s-triazine class of compounds. The enzyme Msd from Mycobacterium smegmatis was taken as a representative candidate from an evolutionarily conserved subgroup that possesses high density of Mycobacterium deaminases. Biochemical investigation reveals that Msd specifically acts on mutagenic nucleobases such as 5-azacytosine and isoguanine and does not accept natural bases as substrates. Determination of the X-ray structure of Msd to a resolution of 1.9 A shows that Msd has fine-tuned its active site such that it is a hybrid of a cytosine as well as a guanine deaminase, thereby conferring Msd the ability to expand its repertoire to both purine and pyrimidine-like mutagens. Mapping of active site residues along with X-ray structures with a series of triazine analogues aids in deciphering the mechanism by which Msd proofreads the base milieu for mutagens. The genome location of the enzyme reveals that Msd is part of a conserved cluster that confers the organism with innate resistance toward select xenobiotics by triggering their efflux.
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Selective Deamination of Mutagens by a Mycobacterial Enzyme.,Gaded V, Anand R J Am Chem Soc. 2017 Aug 9;139(31):10762-10768. doi: 10.1021/jacs.7b04967. Epub, 2017 Jul 28. PMID:28708393<ref>PMID:28708393</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5xko" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Anand, R]]
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[[Category: Mycolicibacterium smegmatis MC2 155]]
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[[Category: Gaded, V M]]
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[[Category: Anand R]]
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[[Category: Cda fold]]
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[[Category: Gaded VM]]
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[[Category: Deaminase]]
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[[Category: Hydrolase]]
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[[Category: Mutagen]]
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Current revision

Crystal structure of native Msmeg3575 deaminase from Mycobacterium smegmatis

PDB ID 5xko

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