3gl0: Difference between revisions

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<StructureSection load='3gl0' size='340' side='right'caption='[[3gl0]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='3gl0' size='340' side='right'caption='[[3gl0]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3gl0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"pseudomonas_maltophilia"_hugh_and_ryschenkow_1961 "pseudomonas maltophilia" hugh and ryschenkow 1961]. 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>
<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" 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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gke|3gke]], [[3gl2|3gl2]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddmC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=40324 "Pseudomonas maltophilia" Hugh and Ryschenkow 1961])</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'>[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>
</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]]
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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=3gl0 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=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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3gl0" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Pseudomonas maltophilia hugh and ryschenkow 1961]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Dumitru, R]]
[[Category: Stenotrophomonas maltophilia]]
[[Category: Jiang, W Z]]
[[Category: Dumitru R]]
[[Category: Weeks, D P]]
[[Category: Jiang WZ]]
[[Category: Wilson, M A]]
[[Category: Weeks DP]]
[[Category: Non-heme mononuclear iron]]
[[Category: Wilson MA]]
[[Category: Oxidoreductase]]
[[Category: Oxygenase]]
[[Category: Rieske protein]]

Revision as of 09:55, 21 February 2024

Crystal structure of dicamba monooxygenase bound to 3,6 dichlorosalicylic acid (DCSA)

3gl0, resolution 1.75Å

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