DDMC_STEMA
ID DDMC_STEMA Reviewed; 339 AA.
AC Q5S3I3;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 84.
DE RecName: Full=Dicamba O-demethylase, oxygenase component {ECO:0000303|PubMed:16535584};
DE EC=1.14.15.- {ECO:0000269|PubMed:15820213, ECO:0000269|PubMed:15855162, ECO:0000269|PubMed:16535584, ECO:0000305|PubMed:19616009};
DE AltName: Full=Dicamba monooxygenase {ECO:0000303|PubMed:15820213};
DE Short=DMO {ECO:0000303|PubMed:19616009};
DE AltName: Full=Three-component Rieske non-heme iron oxygenase system {ECO:0000305};
GN Name=ddmC {ECO:0000303|PubMed:15855162};
OS Stenotrophomonas maltophilia (Pseudomonas maltophilia) (Xanthomonas
OS maltophilia).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Stenotrophomonas; Stenotrophomonas maltophilia group.
OX NCBI_TaxID=40324 {ECO:0000312|EMBL:AAV53699.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP SUBUNIT.
RC STRAIN=DI-6 {ECO:0000312|EMBL:AAV53699.1};
RX PubMed=15855162; DOI=10.1074/jbc.m500597200;
RA Herman P.L., Behrens M., Chakraborty S., Chrastil B.M., Barycki J.,
RA Weeks D.P.;
RT "A three-component dicamba O-demethylase from Pseudomonas maltophilia,
RT strain DI-6: gene isolation, characterization, and heterologous
RT expression.";
RL J. Biol. Chem. 280:24759-24767(2005).
RN [2]
RP PROTEIN SEQUENCE OF 2-28, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, ACTIVITY REGULATION, COFACTOR, AND SUBUNIT.
RC STRAIN=DI-6;
RX PubMed=15820213; DOI=10.1016/j.abb.2005.02.024;
RA Chakraborty S., Behrens M., Herman P.L., Arendsen A.F., Hagen W.R.,
RA Carlson D.L., Wang X.Z., Weeks D.P.;
RT "A three-component dicamba O-demethylase from Pseudomonas maltophilia,
RT strain DI-6: purification and characterization.";
RL Arch. Biochem. Biophys. 437:20-28(2005).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, COFACTOR, AND SUBUNIT.
RC STRAIN=DI-6;
RX PubMed=16535584; DOI=10.1128/aem.63.4.1623-1626.1997;
RA Wang X., Li B., Herman P.L., Weeks D.P.;
RT "A three-component enzyme system catalyzes the O-demethylation of the
RT herbicide dicamba in Pseudomonas maltophilia DI-6.";
RL Appl. Environ. Microbiol. 63:1623-1626(1997).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH IRON ION;
RP IRON-SULFUR (2FE-2S) AND SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY,
RP MUTAGENESIS OF ASN-153; ASP-156; HIS-159; HIS-164 AND ASP-293, ACTIVITY
RP REGULATION, COFACTOR, AND SUBUNIT.
RX PubMed=19616009; DOI=10.1016/j.jmb.2009.07.022;
RA D'Ordine R.L., Rydel T.J., Storek M.J., Sturman E.J., Moshiri F.,
RA Bartlett R.K., Brown G.R., Eilers R.J., Dart C., Qi Y., Flasinski S.,
RA Franklin S.J.;
RT "Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase
RT that catalyzes an exocyclic monooxygenation.";
RL J. Mol. Biol. 392:481-497(2009).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 2-339 IN COMPLEX WITH IRON ION;
RP IRON-SULFUR (2FE-2S) AND SUBSTRATE, COFACTOR, AND SUBUNIT.
RX PubMed=19616011; DOI=10.1016/j.jmb.2009.07.021;
RA Dumitru R., Jiang W.Z., Weeks D.P., Wilson M.A.;
RT "Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase
RT that catalyzes oxidative demethylation.";
RL J. Mol. Biol. 392:498-510(2009).
CC -!- FUNCTION: Component of the dicamba O-demethylase multicomponent enzyme
CC system involved in the degradation of the herbicide dicamba
CC (PubMed:15855162, PubMed:15820213, PubMed:16535584). In vitro,
CC catalyzes the O-demethylation of 2-methoxy-3,6-dichlorobenzoic acid
CC (dicamba) to yield 3,6-dichlorosalicylic acid (DCSA) via an exocyclic
CC monooxygenation (PubMed:15855162, PubMed:15820213, PubMed:16535584,
CC PubMed:19616009). {ECO:0000269|PubMed:15820213,
CC ECO:0000269|PubMed:15855162, ECO:0000269|PubMed:16535584,
CC ECO:0000269|PubMed:19616009}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3,6-dichloro-2-methoxybenzoate + 2 H(+) + O2 + 2 reduced [2Fe-
CC 2S]-[ferredoxin] = 3,6-dichlorosalicylate + formaldehyde + H2O + 2
CC oxidized [2Fe-2S]-[ferredoxin]; Xref=Rhea:RHEA:57016, Rhea:RHEA-
CC COMP:10000, Rhea:RHEA-COMP:10001, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:33737, ChEBI:CHEBI:33738, ChEBI:CHEBI:141349,
CC ChEBI:CHEBI:141350; Evidence={ECO:0000269|PubMed:15820213,
CC ECO:0000269|PubMed:15855162, ECO:0000269|PubMed:16535584,
CC ECO:0000305|PubMed:19616009};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:15820213, ECO:0000269|PubMed:19616009,
CC ECO:0000269|PubMed:19616011, ECO:0000305|PubMed:16535584};
CC Note=Binds 1 [2Fe-2S] cluster per subunit.
CC {ECO:0000269|PubMed:19616009, ECO:0000269|PubMed:19616011};
CC -!- ACTIVITY REGULATION: Activity enhanced by Fe(2+) and Mg(2+) ions.
CC {ECO:0000269|PubMed:15820213, ECO:0000269|PubMed:16535584,
CC ECO:0000269|PubMed:19616009}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=8 uM for dicamba {ECO:0000269|PubMed:15820213};
CC Vmax=150 nmol/min/mg enzyme {ECO:0000269|PubMed:15820213};
CC pH dependence:
CC Optimum pH is between 6.5-7.5. {ECO:0000269|PubMed:15820213};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius.
CC {ECO:0000269|PubMed:15820213};
CC -!- SUBUNIT: Homotrimer (PubMed:15820213, PubMed:19616009,
CC PubMed:19616011). The dicamba O-demethylase multicomponent enzyme
CC system is composed of an oxygenase component (DdmC) and an electron
CC transfer component formed by a ferredoxin reductase (DdmA) and a
CC ferredoxin (DdmB) (PubMed:15855162, PubMed:15820213, PubMed:16535584).
CC In vitro, dicamba O-demethylase assays in which DdmA2 is substituted
CC for DdmA1 demonstrate that the two enzymes possess nearly identical
CC activities (PubMed:15855162). {ECO:0000269|PubMed:15820213,
CC ECO:0000269|PubMed:15855162, ECO:0000269|PubMed:16535584,
CC ECO:0000269|PubMed:19616009, ECO:0000269|PubMed:19616011}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AY786443; AAV53699.1; -; Genomic_DNA.
DR PDB; 3GB4; X-ray; 2.05 A; A/B/C=1-339.
DR PDB; 3GKE; X-ray; 1.75 A; A/B/C=2-339.
DR PDB; 3GL0; X-ray; 1.75 A; A/B/C=2-339.
DR PDB; 3GL2; X-ray; 2.10 A; A/B/C=2-339.
DR PDB; 3GOB; X-ray; 2.05 A; A/B/C=1-339.
DR PDB; 3GTE; X-ray; 1.95 A; A/B/C=1-339.
DR PDB; 3GTS; X-ray; 2.20 A; A/B/C=1-339.
DR PDB; 6VSH; X-ray; 3.00 A; A/B/C=2-339.
DR PDBsum; 3GB4; -.
DR PDBsum; 3GKE; -.
DR PDBsum; 3GL0; -.
DR PDBsum; 3GL2; -.
DR PDBsum; 3GOB; -.
DR PDBsum; 3GTE; -.
DR PDBsum; 3GTS; -.
DR PDBsum; 6VSH; -.
DR AlphaFoldDB; Q5S3I3; -.
DR SMR; Q5S3I3; -.
DR EvolutionaryTrace; Q5S3I3; -.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004497; F:monooxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0019439; P:aromatic compound catabolic process; IEA:UniProtKB-KW.
DR Gene3D; 2.102.10.10; -; 1.
DR InterPro; IPR017941; Rieske_2Fe-2S.
DR InterPro; IPR036922; Rieske_2Fe-2S_sf.
DR InterPro; IPR044043; VanA_C_cat.
DR Pfam; PF00355; Rieske; 1.
DR Pfam; PF19112; VanA_C; 1.
DR SUPFAM; SSF50022; SSF50022; 1.
DR PROSITE; PS51296; RIESKE; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Aromatic hydrocarbons catabolism;
KW Direct protein sequencing; Iron; Iron-sulfur; Metal-binding; Monooxygenase;
KW Oxidoreductase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:15820213"
FT CHAIN 2..339
FT /note="Dicamba O-demethylase, oxygenase component"
FT /id="PRO_0000445255"
FT DOMAIN 8..110
FT /note="Rieske"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 48
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTE, ECO:0007744|PDB:3GTS"
FT BINDING 50
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTE, ECO:0007744|PDB:3GTS"
FT BINDING 67
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTE, ECO:0007744|PDB:3GTS"
FT BINDING 70
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTE, ECO:0007744|PDB:3GTS"
FT BINDING 159
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTE, ECO:0007744|PDB:3GTS"
FT BINDING 164
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTE, ECO:0007744|PDB:3GTS"
FT BINDING 229
FT /ligand="3,6-dichloro-2-methoxybenzoate"
FT /ligand_id="ChEBI:CHEBI:141349"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTS"
FT BINDING 250
FT /ligand="3,6-dichloro-2-methoxybenzoate"
FT /ligand_id="ChEBI:CHEBI:141349"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTS"
FT BINDING 284
FT /ligand="3,6-dichloro-2-methoxybenzoate"
FT /ligand_id="ChEBI:CHEBI:141349"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GTS"
FT BINDING 293
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:19616009,
FT ECO:0000269|PubMed:19616011, ECO:0007744|PDB:3GB4,
FT ECO:0007744|PDB:3GKE, ECO:0007744|PDB:3GL0,
FT ECO:0007744|PDB:3GL2, ECO:0007744|PDB:3GOB,
FT ECO:0007744|PDB:3GTE, ECO:0007744|PDB:3GTS"
FT SITE 153
FT /note="Plays a role in the stabilization of the metal
FT coordination"
FT /evidence="ECO:0000269|PubMed:19616009"
FT MUTAGEN 153
FT /note="N->A: Strong reduction of O-demethylase activity."
FT /evidence="ECO:0000269|PubMed:19616009"
FT MUTAGEN 156
FT /note="D->N: Strong reduction of O-demethylase activity."
FT /evidence="ECO:0000269|PubMed:19616009"
FT MUTAGEN 159
FT /note="H->N: Loss of O-demethylase activity."
FT /evidence="ECO:0000269|PubMed:19616009"
FT MUTAGEN 164
FT /note="H->N: Loss of O-demethylase activity."
FT /evidence="ECO:0000269|PubMed:19616009"
FT MUTAGEN 293
FT /note="D->N: Loss of O-demethylase activity."
FT /evidence="ECO:0000269|PubMed:19616009"
FT STRAND 9..12
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 14..16
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:3GL0"
FT STRAND 22..26
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 29..35
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 41..47
FT /evidence="ECO:0007829|PDB:3GKE"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 64..66
FT /evidence="ECO:0007829|PDB:3GKE"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 120..122
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 127..130
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 134..145
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 147..155
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 160..163
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 165..168
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 173..175
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 177..182
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 184..196
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 200..205
FT /evidence="ECO:0007829|PDB:3GKE"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 213..222
FT /evidence="ECO:0007829|PDB:3GKE"
FT TURN 223..225
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 226..235
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 243..256
FT /evidence="ECO:0007829|PDB:3GKE"
FT STRAND 259..271
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 275..288
FT /evidence="ECO:0007829|PDB:3GKE"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 292..302
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 304..309
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 318..320
FT /evidence="ECO:0007829|PDB:3GKE"
FT HELIX 321..338
FT /evidence="ECO:0007829|PDB:3GKE"
SQ SEQUENCE 339 AA; 37299 MW; 7A86792D83DE4C3B CRC64;
MTFVRNAWYV AALPEELSEK PLGRTILDTP LALYRQPDGV VAALLDICPH RFAPLSDGIL
VNGHLQCPYH GLEFDGGGQC VHNPHGNGAR PASLNVRSFP VVERDALIWI WPGDPALADP
GAIPDFGCRV DPAYRTVGGY GHVDCNYKLL VDNLMDLGHA QYVHRANAQT DAFDRLEREV
IVGDGEIQAL MKIPGGTPSV LMAKFLRGAN TPVDAWNDIR WNKVSAMLNF IAVAPEGTPK
EQSIHSRGTH ILTPETEASC HYFFGSSRNF GIDDPEMDGV LRSWQAQALV KEDKVVVEAI
ERRRAYVEAN GIRPAMLSCD EAAVRVSREI EKLEQLEAA
