3gl0
From Proteopedia
(Difference between revisions)
| (3 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| + | |||
==Crystal structure of dicamba monooxygenase bound to 3,6 dichlorosalicylic acid (DCSA)== | ==Crystal structure of dicamba monooxygenase bound to 3,6 dichlorosalicylic acid (DCSA)== | ||
| - | <StructureSection load='3gl0' size='340' side='right' caption='[[3gl0]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='3gl0' size='340' side='right'caption='[[3gl0]], [[Resolution|resolution]] 1.75Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3gl0]] is a 3 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[3gl0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Stenotrophomonas_maltophilia Stenotrophomonas maltophilia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GL0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HXX:3,6-DICHLORO-2-HYDROXYBENZOIC+ACID'>HXX</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HXX:3,6-DICHLORO-2-HYDROXYBENZOIC+ACID'>HXX</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=3gl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gl0 OCA], [https://pdbe.org/3gl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gl0 RCSB], [https://www.ebi.ac.uk/pdbsum/3gl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gl0 ProSAT]</span></td></tr> | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DDMC_STEMA DDMC_STEMA] Component of the dicamba O-demethylase multicomponent enzyme system involved in the degradation of the herbicide dicamba (PubMed:15855162, PubMed:15820213, PubMed:16535584). In vitro, catalyzes the O-demethylation of 2-methoxy-3,6-dichlorobenzoic acid (dicamba) to yield 3,6-dichlorosalicylic acid (DCSA) via an exocyclic monooxygenation (PubMed:15855162, PubMed:15820213, PubMed:16535584, PubMed:19616009).<ref>PMID:15820213</ref> <ref>PMID:15855162</ref> <ref>PMID:16535584</ref> <ref>PMID:19616009</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gl/3gl0_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gl/3gl0_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
| - | </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/ | + | </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=3gl0 ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Dicamba (3,6-dichloro-2-methoxybenzoic acid) is a widely used herbicide that is efficiently degraded by soil microbes. These microbes use a novel Rieske nonheme oxygenase, dicamba monooxygenase (DMO), to catalyze the oxidative demethylation of dicamba to 3,6-dichlorosalicylic acid (DCSA) and formaldehyde. We have determined the crystal structures of DMO in the free state, bound to its substrate dicamba, and bound to the product DCSA at 2.10-1.75 A resolution. The structures show that the DMO active site uses a combination of extensive hydrogen bonding and steric interactions to correctly orient chlorinated, ortho-substituted benzoic-acid-like substrates for catalysis. Unlike other Rieske aromatic oxygenases, DMO oxygenates the exocyclic methyl group, rather than the aromatic ring, of its substrate. This first crystal structure of a Rieske demethylase shows that the Rieske oxygenase structural scaffold can be co-opted to perform varied types of reactions on xenobiotic substrates. | ||
| - | |||
| - | Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation.,Dumitru R, Jiang WZ, Weeks DP, Wilson MA J Mol Biol. 2009 Sep 18;392(2):498-510. Epub 2009 Jul 15. PMID:19616011<ref>PMID:19616011</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Stenotrophomonas maltophilia]] | [[Category: Stenotrophomonas maltophilia]] | ||
| - | [[Category: Dumitru | + | [[Category: Dumitru R]] |
| - | [[Category: Jiang | + | [[Category: Jiang WZ]] |
| - | [[Category: Weeks | + | [[Category: Weeks DP]] |
| - | [[Category: Wilson | + | [[Category: Wilson MA]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Crystal structure of dicamba monooxygenase bound to 3,6 dichlorosalicylic acid (DCSA)
| |||||||||||
