3gl0: Difference between revisions

Latest revision as of 09:22, 13 August 2026

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

Structural highlights

3gl0 is a 3 chain structure with sequence from Stenotrophomonas maltophilia. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:	EDO, FE, FES, HXX, OXY
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[5]

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

References

↑ Chakraborty S, Behrens M, Herman PL, Arendsen AF, Hagen WR, Carlson DL, Wang XZ, Weeks DP. A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: purification and characterization. Arch Biochem Biophys. 2005 May 1;437(1):20-8. doi: 10.1016/j.abb.2005.02.024. PMID:15820213 doi:https://dx.doi.org/10.1016/j.abb.2005.02.024
↑ Herman PL, Behrens M, Chakraborty S, Chrastil BM, Barycki J, Weeks DP. A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: gene isolation, characterization, and heterologous expression. J Biol Chem. 2005 Jul 1;280(26):24759-67. doi: 10.1074/jbc.M500597200. Epub 2005 , Apr 26. PMID:15855162 doi:https://dx.doi.org/10.1074/jbc.M500597200
↑ Wang X, Li B, Herman PL, Weeks DP. A Three-Component Enzyme System Catalyzes the O Demethylation of the Herbicide Dicamba in Pseudomonas maltophilia DI-6. Appl Environ Microbiol. 1997 Apr;63(4):1623-6. PMID:16535584
↑ D'Ordine RL, Rydel TJ, Storek MJ, Sturman EJ, Moshiri F, Bartlett RK, Brown GR, Eilers RJ, Dart C, Qi Y, Flasinski S, Franklin SJ. Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase that catalyzes an exocyclic monooxygenation. J Mol Biol. 2009 Sep 18;392(2):481-97. Epub 2009 Jul 15. PMID:19616009 doi:10.1016/j.jmb.2009.07.022
↑ Dumitru R, Jiang WZ, Weeks DP, Wilson MA. Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation. J Mol Biol. 2009 Sep 18;392(2):498-510. Epub 2009 Jul 15. PMID:19616011 doi:10.1016/j.jmb.2009.07.021

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Chakraborty S, Behrens M, Herman PL, Arendsen AF, Hagen WR, Carlson DL, Wang XZ, Weeks DP. A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: purification and characterization. Arch Biochem Biophys. 2005 May 1;437(1):20-8. doi: 10.1016/j.abb.2005.02.024. PMID:15820213 doi:https://dx.doi.org/10.1016/j.abb.2005.02.024

[2] Herman PL, Behrens M, Chakraborty S, Chrastil BM, Barycki J, Weeks DP. A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: gene isolation, characterization, and heterologous expression. J Biol Chem. 2005 Jul 1;280(26):24759-67. doi: 10.1074/jbc.M500597200. Epub 2005 , Apr 26. PMID:15855162 doi:https://dx.doi.org/10.1074/jbc.M500597200

[3] Wang X, Li B, Herman PL, Weeks DP. A Three-Component Enzyme System Catalyzes the O Demethylation of the Herbicide Dicamba in Pseudomonas maltophilia DI-6. Appl Environ Microbiol. 1997 Apr;63(4):1623-6. PMID:16535584

[4] D'Ordine RL, Rydel TJ, Storek MJ, Sturman EJ, Moshiri F, Bartlett RK, Brown GR, Eilers RJ, Dart C, Qi Y, Flasinski S, Franklin SJ. Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase that catalyzes an exocyclic monooxygenation. J Mol Biol. 2009 Sep 18;392(2):481-97. Epub 2009 Jul 15. PMID:19616009 doi:10.1016/j.jmb.2009.07.022

[5] Dumitru R, Jiang WZ, Weeks DP, Wilson MA. Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation. J Mol Biol. 2009 Sep 18;392(2):498-510. Epub 2009 Jul 15. PMID:19616011 doi:10.1016/j.jmb.2009.07.021

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[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
 ==Crystal structure of dicamba monooxygenase bound to 3,6 dichlorosalicylic acid (DCSA)==
-<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 ==
-<table><tr><td colspan='2'>[[3gl0]] is a 3 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/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"><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">[[3gke|3gke]], [[3gl2|3gl2]]</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 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gl0 OCA], [http://pdbe.org/3gl0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gl0 RCSB], [http://www.ebi.ac.uk/pdbsum/3gl0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gl0 ProSAT]</span></td></tr>
 </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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
    <jmolCheckbox>
      <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/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Pseudomonas maltophilia hugh and ryschenkow 1961]]
+[[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]]

3gl0: Difference between revisions

Latest revision as of 09:22, 13 August 2026

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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