SDPA_DELAC
ID SDPA_DELAC Reviewed; 292 AA.
AC P83309; Q67FS3;
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=(S)-phenoxypropionate/alpha-ketoglutarate-dioxygenase {ECO:0000303|PubMed:12501996};
DE Short=SdpA {ECO:0000303|PubMed:12501996};
DE EC=1.14.11.43 {ECO:0000269|Ref.5};
DE AltName: Full=(S)-dichlorprop/(S)-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=sdpA {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 1-25; 100-106 AND 170-182, 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 S-dichlorprop ((S)-2-(2,4-dichlorophenoxy)propionate)(S-
CC 2,4-DP) and S-mecoprop ((S)-2-(4-chloro-2-methylphenoxy)propionate)(S-
CC 2,4-MCPP). It can also accept (RS)-2-(4-chlorophenoxy)propionate, (RS)-
CC 2-(m-chlorophenoxy)propionate and phenoxyacetate derivatives such as
CC 2,4-dichlorophenoxyacetate (2,4-D), 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=(S)-2-(4-chloro-2-methylphenoxy)propanoate + 2-oxoglutarate +
CC O2 = 2-methyl-4-chlorophenol + CO2 + pyruvate + succinate;
CC Xref=Rhea:RHEA:37831, ChEBI:CHEBI:1800, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:75285; EC=1.14.11.43;
CC Evidence={ECO:0000269|Ref.5};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-(2,4-dichlorophenoxy)propanoate + 2-oxoglutarate + O2 =
CC 2,4-dichlorophenol + CO2 + pyruvate + succinate;
CC Xref=Rhea:RHEA:37827, ChEBI:CHEBI:15361, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16738, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:75287; EC=1.14.11.43;
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=11.5 uM for (RS)-2-(m-chlorophenoxy)propionate (at pH 6 and 25
CC degrees Celsius) {ECO:0000269|Ref.5};
CC KM=21.8 uM for S-2,4-MCPP (at pH 6 and 25 degrees Celsius)
CC {ECO:0000269|Ref.5};
CC KM=24.1 uM for alpha-ketoglutarate (at pH 6 and 25 degrees Celsius)
CC {ECO:0000269|Ref.5};
CC KM=49 uM for S-2,4-DP (at pH 6 and 25 degrees Celsius)
CC {ECO:0000269|Ref.5};
CC KM=68.3 uM for (RS)-2-(4-chlorophenoxy)propionate (at pH 6 and 25
CC degrees Celsius) {ECO:0000269|Ref.5};
CC KM=122.8 uM for 2,4-D (at pH 6 and 25 degrees Celsius)
CC {ECO:0000269|Ref.5};
CC Note=kcat is 50 min(-1) for dioxygenase activity with S-2,4-DP (at pH
CC 6 and 25 degrees Celsius). kcat is 46 min(-1) for dioxygenase
CC activity with S-2,4-MCPP (at pH 6 and 25 degrees Celsius). kcat is 36
CC min(-1) for dioxygenase activity with 2,4-D (at pH 6 and 25 degrees
CC Celsius). kcat is 17 min(-1) for dioxygenase activity with (RS)-2-(4-
CC chlorophenoxy)propionate (at pH 6 and 25 degrees Celsius). kcat is 15
CC min(-1) for dioxygenase activity with (RS)-2-(m-
CC chlorophenoxy)propionate (at pH 6 and 25 degrees Celsius). kcat is
CC 1.7 min(-1) for dioxygenase activity with alpha-ketoglutarate (at pH
CC 6 and 25 degrees Celsius). {ECO:0000269|Ref.5};
CC pH dependence:
CC Optimum pH is about 6. {ECO:0000269|Ref.5};
CC Temperature dependence:
CC Optimum temperature is 25 degrees Celsius. {ECO:0000269|Ref.5};
CC -!- PATHWAY: Xenobiotic degradation; 2-(2,4-dichlorophenoxy)propanoate
CC degradation. {ECO:0000305|Ref.5}.
CC -!- SUBUNIT: Monomer. {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; AAP88277.1; -; Genomic_DNA.
DR AlphaFoldDB; P83309; -.
DR SMR; P83309; -.
DR KEGG; ag:AAP88277; -.
DR BRENDA; 1.14.11.43; 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 Dioxygenase; Direct protein sequencing; Iron; Metal-binding;
KW Oxidoreductase; Plasmid; Vitamin C.
FT CHAIN 1..292
FT /note="(S)-phenoxypropionate/alpha-ketoglutarate-
FT dioxygenase"
FT /id="PRO_0000097650"
FT BINDING 108
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 110
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 135
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 247
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 262
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 273
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT CONFLICT 105
FT /note="M -> T (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 170
FT /note="K -> G (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 292 AA; 31658 MW; 1E158CF1386B139F CRC64;
MQTTLQITPT GATLGATVTG VHLATLDDAG FAALHAAWLQ HALLIFPGQH LSNDQQITFA
KRFGAIERIG GGDIVAISNV KADGTVRQHS PAEWDDMMKV IVGNMAWHAD STYMPVMAQG
AVFSAEVVPA VGGRTCFADM RAAYDALDEA TRALVHQRSA RHSLVYSQSK LGHVQQAGSA
YIGYGMDTTA TPLRPLVKVH PETGRPSLLI GRHAHAIPGM DAAESERFLE GLVDWACQAP
RVHAHQWAAG DVVVWDNRCL LHRAEPWDFK LPRVMWHSRL AGRPETEGAA LV
