5xkr: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 5xkr is ~~ON HOLD until Paper~~ Publication

==Crystal structure of Msmeg3575 in complex with benzoguanamine==

== Structural highlights ==

<table><tr><td colspan='2'>[[5xkr]] is a 4 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=5XKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XKR 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]] 1.38Å</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=BZE:6-PHENYL-1,3,5-TRIAZINE-2,4-DIAMINE'>BZE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5xkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkr OCA], [https://pdbe.org/5xkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xkr RCSB], [https://www.ebi.ac.uk/pdbsum/5xkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkr ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0QY90_MYCS2 A0QY90_MYCS2]

== Publication Abstract from PubMed ==

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.

~~Authors~~:

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>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Mycolicibacterium smegmatis MC2 155]]

[[Category: Anand R]]

[[Category: Gaded VM]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5xkr is ON HOLD  until Paper Publication
+==Crystal structure of Msmeg3575 in complex with benzoguanamine==
+<StructureSection load='5xkr' size='340' side='right'caption='[[5xkr]], [[Resolution|resolution]] 1.38&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5xkr]] is a 4 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=5XKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XKR 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]] 1.38&#8491;</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=BZE:6-PHENYL-1,3,5-TRIAZINE-2,4-DIAMINE'>BZE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5xkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkr OCA], [https://pdbe.org/5xkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xkr RCSB], [https://www.ebi.ac.uk/pdbsum/5xkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0QY90_MYCS2 A0QY90_MYCS2]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-Authors:
+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>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5xkr" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Mycolicibacterium smegmatis MC2 155]]
+[[Category: Anand R]]
+[[Category: Gaded VM]]