RDPA_DELAC
ID RDPA_DELAC Reviewed; 295 AA.
AC P83310; Q67FR0;
DT 10-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 29-OCT-2014, sequence version 2.
DT 03-AUG-2022, entry version 52.
DE RecName: Full=(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase {ECO:0000303|PubMed:12501996};
DE Short=RdpA {ECO:0000303|PubMed:12501996};
DE EC=1.14.11.44 {ECO:0000269|Ref.5};
DE AltName: Full=(R)-dichlorprop/(R)-mecoprop dioxygenase {ECO:0000303|PubMed:12501996};
DE AltName: Full=Alpha-ketoglutarate-dependent dioxygenase {ECO:0000303|PubMed:12501996};
DE AltName: Full=Dichlorprop/alpha-ketoglutarate-dioxygenase {ECO:0000303|PubMed:12501996};
DE AltName: Full=Mecoprop/alpha-ketoglutarate-dioxygenase {ECO:0000303|PubMed:12501996};
GN Name=rdpA {ECO:0000303|PubMed:12501996};
OS Delftia acidovorans (Pseudomonas acidovorans) (Comamonas acidovorans).
OG Plasmid pMC1.
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Delftia.
OX NCBI_TaxID=80866;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MC1; PLASMID=pMC1;
RX PubMed=15345421; DOI=10.1128/aem.70.9.5357-5365.2004;
RA Schleinitz K.M., Kleinsteuber S., Vallaeys T., Babel W.;
RT "Localization and characterization of two novel genes encoding
RT stereospecific dioxygenases catalyzing 2(2,4-dichlorophenoxy)propionate
RT cleavage in Delftia acidovorans MC1.";
RL Appl. Environ. Microbiol. 70:5357-5365(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MC1; PLASMID=pMC1;
RA Schleinitz K.M., Kleinsteuber S., Vallaeys T., Babel W.;
RT "Genetic background of enantiospecific 2,4-dichlorophenoxypropionate
RT cleavage in Delftia acidovorans MC1.";
RL Submitted (SEP-2009) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MC1; PLASMID=pMC1;
RA Schleinitz K.M., Vallaeys T., Kleinsteuber S.;
RT "Structural analysis of ISCR8, a subgroup of IS91-like elements.";
RL Submitted (SEP-2009) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP PROTEIN SEQUENCE OF 1-24 AND 43-115, FUNCTION, AND SUBUNIT.
RC STRAIN=MC1;
RX PubMed=12501996; DOI=10.1078/0944-5013-00164;
RA Westendorf A., Benndorf D., Mueller R.H., Babel W.;
RT "The two enantiospecific dichlorprop/alpha-ketoglutarate-dioxygenases from
RT Delftia acidovorans MC1 -- protein and sequence data of RdpA and SdpA.";
RL Microbiol. Res. 157:317-322(2002).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP ACTIVITY REGULATION, PATHWAY, AND SUBSTRATE SPECIFICITY.
RC STRAIN=MC1;
RA Westendorf A., Mueller R.H., Babel W.;
RT "Purification and characterisation of the enantiospecific dioxygenases from
RT Delftia acidovorans MC1 initiating the degradation of phenoxypropionate and
RT phenoxyacetate herbicides.";
RL Acta Biotechnol. 23:3-17(2003).
RN [6]
RP INDUCTION.
RC STRAIN=MC1;
RX PubMed=15073309; DOI=10.1099/mic.0.26774-0;
RA Benndorf D., Davidson I., Babel W.;
RT "Regulation of catabolic enzymes during long-term exposure of Delftia
RT acidovorans MC1 to chlorophenoxy herbicides.";
RL Microbiology 150:1005-1014(2004).
CC -!- FUNCTION: Involved in the degradation of the phenoxypropionate
CC herbicides. Catalyzes the enantiospecific cleavage of the ether bond in
CC the herbicid R-dichlorprop ((R)-2-(2,4-dichlorophenoxy)propionate)(R-
CC 2,4-DP) and R-mecoprop ((R)-2-(4-chloro-2-methylphenoxy)propionate)(R-
CC 2,4-MCPP). It can also accept (RS)-2-(2,4,5-
CC trichlorophenoxy)propionate, (RS)-2-(4-chlorophenoxy)propionate, (RS)-
CC 2-(m-chlorophenoxy)propionate, however it can only accept 2-
CC oxoglutarate as oxygen acceptor. {ECO:0000269|Ref.5,
CC ECO:0000303|PubMed:12501996}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-2-(4-chloro-2-methylphenoxy)propanoate + 2-oxoglutarate +
CC O2 = 2-methyl-4-chlorophenol + CO2 + pyruvate + succinate;
CC Xref=Rhea:RHEA:37815, ChEBI:CHEBI:1800, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:75284; EC=1.14.11.44;
CC Evidence={ECO:0000269|Ref.5};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-(2,4-dichlorophenoxy)propanoate + 2-oxoglutarate + O2 =
CC 2,4-dichlorophenol + CO2 + pyruvate + succinate;
CC Xref=Rhea:RHEA:37823, ChEBI:CHEBI:15361, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16738, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:75288; EC=1.14.11.44;
CC Evidence={ECO:0000269|Ref.5};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875; Evidence={ECO:0000269|Ref.5};
CC -!- COFACTOR:
CC Name=L-ascorbate; Xref=ChEBI:CHEBI:38290; Evidence={ECO:0000269|Ref.5};
CC -!- ACTIVITY REGULATION: Inhibited by divalent cations, most significantly
CC by copper and nickel, and by diethylpyrocarbonate (DEPC).
CC {ECO:0000269|Ref.5}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=27.8 uM for alpha-ketoglutarate (at pH 6 and 30 degrees Celsius))
CC {ECO:0000269|Ref.5};
CC KM=54.9 uM for R-2,4-DP (at pH 6 and 30 degrees Celsius)
CC {ECO:0000269|Ref.5};
CC KM=30 uM for R-2,4-MCPP (at pH 6 and 30 degrees Celsius)
CC {ECO:0000269|Ref.5};
CC KM=130.8 uM for (RS)-2-(2,4,5-trichlorophenoxy)propionate (at pH 6
CC and 30 degrees Celsius) {ECO:0000269|Ref.5};
CC KM=131.4 uM for (RS)-2-(4-chlorophenoxy)propionate (at pH 6 and 30
CC degrees Celsius) {ECO:0000269|Ref.5};
CC KM=176.2 uM for (RS)-2-(m-chlorophenoxy)propionate (at pH 6 and 30
CC degrees Celsius) {ECO:0000269|Ref.5};
CC KM=261 uM for S-2,4-MCPP (at pH 6 and 30 degrees Celsius)
CC {ECO:0000269|Ref.5};
CC KM=1305 uM for 2,4-dichlorophenoxyacetate (at pH 6 and 30 degrees
CC Celsius) {ECO:0000269|Ref.5};
CC Note=kcat is 65.2 min(-1) for dioxygenase activity with (RS)-2-(4-
CC chlorophenoxy)propionate (at pH 6 and 30 degrees Celsius). kcat is
CC 55.2 min(-1) for dioxygenase activity with R-2,4-DP (at pH 6 and 30
CC degrees Celsius). kcat is 50 min(-1) for dioxygenase activity with
CC (RS)-2-(2,4,5-trichlorophenoxy)propionate (at pH 6 and 30 degrees
CC Celsius). kcat is 34.4 min(-1) for dioxygenase activity with R-2,4-
CC MCPP and (RS)-2-(m-chlorophenoxy)propionate (at pH 6 and 30 degrees
CC Celsius). kcat is 20 min(-1) for dioxygenase activity with alpha-
CC ketoglutarate (at pH 6 and 30 degrees Celsius). kcat is 7.6 min(-1)
CC for dioxygenase activity with 2,4-dichlorophenoxyacetate (at pH 6 and
CC 30 degrees Celsius). kcat is 3.8 min(-1) for dioxygenase activity
CC with S-2,4-MCPP (at pH 6 and 30 degrees Celsius).
CC {ECO:0000269|Ref.5};
CC pH dependence:
CC Optimum pH is about 6. {ECO:0000269|Ref.5};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius. {ECO:0000269|Ref.5};
CC -!- PATHWAY: Xenobiotic degradation; 2-(2,4-dichlorophenoxy)propanoate
CC degradation. {ECO:0000305|Ref.5}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:12501996}.
CC -!- INDUCTION: Repressed during growth on high concentrations of 2,4-
CC dichlorophenoxypropionic acid (2,4-DCPP).
CC {ECO:0000269|PubMed:15073309}.
CC -!- SIMILARITY: Belongs to the TfdA dioxygenase family. {ECO:0000305}.
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DR EMBL; AY327575; AAP88290.1; -; Genomic_DNA.
DR PDB; 5BK9; X-ray; 1.51 A; A/B=1-295.
DR PDB; 5BKB; X-ray; 1.58 A; A/B=1-295.
DR PDB; 5BKC; X-ray; 1.80 A; A/B=1-295.
DR PDB; 5BKD; X-ray; 1.90 A; A/B=1-295.
DR PDBsum; 5BK9; -.
DR PDBsum; 5BKB; -.
DR PDBsum; 5BKC; -.
DR PDBsum; 5BKD; -.
DR AlphaFoldDB; P83310; -.
DR SMR; P83310; -.
DR KEGG; ag:AAP88290; -.
DR BRENDA; 1.14.11.44; 1586.
DR UniPathway; UPA00348; -.
DR GO; GO:0051213; F:dioxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0031418; F:L-ascorbic acid binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.60.130.10; -; 1.
DR InterPro; IPR042098; TauD-like_sf.
DR InterPro; IPR003819; TauD/TfdA-like.
DR Pfam; PF02668; TauD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Dioxygenase; Direct protein sequencing; Iron; Metal-binding;
KW Oxidoreductase; Plasmid; Vitamin C.
FT CHAIN 1..295
FT /note="(R)-phenoxypropionate/alpha-ketoglutarate-
FT dioxygenase"
FT /id="PRO_0000097210"
FT BINDING 111
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 113
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 138
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 255
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 270
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 281
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT CONFLICT 23..24
FT /note="VL -> GV (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 72..84
FT /note="RRFGPVDPVPLLK -> ETLSPTMQATIEGLN (in Ref. 4; AA
FT sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 114..115
FT /note="ST -> II (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 8..11
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 13..24
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 26..30
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 39..52
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 53..57
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 64..72
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 89..97
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:5BK9"
FT TURN 113..116
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 122..130
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 133..135
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 138..142
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 143..148
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 152..158
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 162..165
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 168..171
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 173..177
FT /evidence="ECO:0007829|PDB:5BK9"
FT TURN 184..186
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 192..196
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 199..206
FT /evidence="ECO:0007829|PDB:5BK9"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 213..215
FT /evidence="ECO:0007829|PDB:5BK9"
FT TURN 219..221
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 222..225
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 230..244
FT /evidence="ECO:0007829|PDB:5BK9"
FT HELIX 247..249
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 250..253
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 260..264
FT /evidence="ECO:0007829|PDB:5BK9"
FT TURN 265..267
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 268..272
FT /evidence="ECO:0007829|PDB:5BK9"
FT STRAND 281..288
FT /evidence="ECO:0007829|PDB:5BK9"
SQ SEQUENCE 295 AA; 33213 MW; 9FAA1CB29DD426E9 CRC64;
MHAALSPLSQ RFERIAVQPL TGVLGAEITG VDLREPLDDS TWNEILDAFH TYQVIYFPGQ
AITNEQHIAF SRRFGPVDPV PLLKSIEGYP EVQMIRREAN ESGRVIGDDW HTDSTFLDAP
PAAVVMRAID VPEHGGDTGF LSMYTAWETL SPTMQATIEG LNVVHSATRV FGSLYQAQNR
RFSNTSVKVM DVDAGDRETV HPLVVTHPGS GRKGLYVNQV YCQRIEGMTD AESKPLLQFL
YEHATRFDFT CRVRWKKDQV LVWDNLCTMH RAVPDYAGKF RYLTRTTVGG VRPAR
