RDPA_SPHHM
ID RDPA_SPHHM Reviewed; 295 AA.
AC Q8KSC8;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2004, sequence version 2.
DT 03-AUG-2022, entry version 62.
DE RecName: Full=(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase {ECO:0000303|PubMed:15345421};
DE Short=RdpA {ECO:0000303|PubMed:15345421};
DE EC=1.14.11.44 {ECO:0000269|PubMed:16731970, ECO:0000269|PubMed:16820480};
DE AltName: Full=(R)-dichlorprop/(R)-mecoprop dioxygenase {ECO:0000303|PubMed:16820480};
DE AltName: Full=Alpha-ketoglutarate-dependent dioxygenase {ECO:0000303|PubMed:16820480};
DE AltName: Full=Dichlorprop/alpha-ketoglutarate-dioxygenase {ECO:0000303|PubMed:16820480};
DE AltName: Full=Mecoprop/alpha-ketoglutarate-dioxygenase {ECO:0000303|PubMed:16820480};
GN Name=rdpA {ECO:0000303|PubMed:15345421};
OS Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 /
OS MH) (Sphingomonas herbicidovorans).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingobium.
OX NCBI_TaxID=1219045;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=ATCC 700291 / DSM 11019 / NBRC 16415 / MH;
RX PubMed=11423952; DOI=10.1038/sj.jim.2900751;
RA Kohler H.P.E.;
RT "Sphingomonas herbicidovorans MH: a versatile phenoxyalkanoic acid
RT herbicide degrader.";
RL J. Ind. Microbiol. Biotechnol. 23:336-340(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 700291 / DSM 11019 / NBRC 16415 / MH;
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 [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 700291 / DSM 11019 / NBRC 16415 / MH;
RX PubMed=15466552; DOI=10.1128/aem.70.10.6066-6075.2004;
RA Mueller T.A., Byrde S.M., Werlen C., van der Meer J.R., Kohler H.P.E.;
RT "Genetic analysis of phenoxyalkanoic acid degradation in Sphingomonas
RT herbicidovorans MH.";
RL Appl. Environ. Microbiol. 70:6066-6075(2004).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP COFACTOR, SUBSTRATE SPECIFICITY, AND PATHWAY.
RX PubMed=16820480; DOI=10.1128/aem.02758-05;
RA Mueller T.A., Fleischmann T., van der Meer J.R., Kohler H.P.;
RT "Purification and characterization of two enantioselective alpha-
RT ketoglutarate-dependent dioxygenases, RdpA and SdpA, from Sphingomonas
RT herbicidovorans MH.";
RL Appl. Environ. Microbiol. 72:4853-4861(2006).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF VAL-80; LEU-83; GLN-93; ILE-106; GLY-107; PHE-171; TYR-221
RP AND ARG-285.
RX PubMed=16731970; DOI=10.1110/ps.052059406;
RA Mueller T.A., Zavodszky M.I., Feig M., Kuhn L.A., Hausinger R.P.;
RT "Structural basis for the enantiospecificities of R- and S-specific
RT phenoxypropionate/alpha-ketoglutarate dioxygenases.";
RL Protein Sci. 15:1356-1368(2006).
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)-4-chlorophenoxypropanoate, however
CC it can only accept 2-oxoglutarate as oxygen acceptor.
CC {ECO:0000269|PubMed:16731970, ECO:0000269|PubMed:16820480,
CC ECO:0000303|PubMed:11423952}.
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|PubMed:16731970, ECO:0000269|PubMed:16820480,
CC ECO:0000303|PubMed:11423952};
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|PubMed:16731970, ECO:0000269|PubMed:16820480};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC Evidence={ECO:0000269|PubMed:16820480};
CC -!- COFACTOR:
CC Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
CC Evidence={ECO:0000250|UniProtKB:Q67FR0};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.8 uM for alpha-ketoglutarate (at pH 6.75 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16820480};
CC KM=98.8 uM for R-2,4-MCPP (at pH 6.75 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16820480};
CC KM=163.7 uM for R-2,4-DP (at pH 6.75 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16820480};
CC KM=262.4 uM for (RS)-4-chlorophenoxypropanoate (at pH 6.75 and 30
CC degrees Celsius) {ECO:0000269|PubMed:16820480};
CC KM=380 uM for R-2,4-MCPP (at pH 6.75 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16731970};
CC Note=kcat is 114.2 min(-1) for dioxygenase activity with R-2,4-MCPP
CC (at pH 6.75 and 30 degrees Celsius). kcat is 135.6 min(-1) for
CC dioxygenase activity with alpha-ketoglutarate (at pH 6.75 and 30
CC degrees Celsius). kcat is 170.1 min(-1) for dioxygenase activity with
CC R-2,4-DP (at pH 6.75 and 30 degrees Celsius). kcat is 241.9 min(-1)
CC for dioxygenase activity with (RS)-4-chlorophenoxypropanoate (at pH
CC 6.75 and 30 degrees Celsius). kcat is 252 min(-1) for dioxygenase
CC activity with R-2,4-MCPP (at pH 6.75 and 30 degrees Celsius).
CC {ECO:0000269|PubMed:16731970, ECO:0000269|PubMed:16820480};
CC pH dependence:
CC Optimum pH is about 6.5. {ECO:0000269|PubMed:16820480};
CC Temperature dependence:
CC Optimum temperature is between 35 and 40 degrees Celsius.
CC {ECO:0000269|PubMed:16820480};
CC -!- PATHWAY: Xenobiotic degradation; 2-(2,4-dichlorophenoxy)propanoate
CC degradation. {ECO:0000305|PubMed:16820480}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:16820480}.
CC -!- SIMILARITY: Belongs to the TfdA dioxygenase family. {ECO:0000305}.
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; AF516752; AAM90965.2; -; Genomic_DNA.
DR EMBL; AJ628859; CAF32811.1; -; Genomic_DNA.
DR RefSeq; WP_031942865.1; NZ_BCZD01000078.1.
DR PDB; 6D0O; X-ray; 2.30 A; A/B/C/D=1-295.
DR PDB; 6D1O; X-ray; 2.70 A; A/B/C/D/E/F/G/H=1-295.
DR PDB; 6D3H; X-ray; 2.03 A; A/B/I/M=1-295.
DR PDB; 6D3I; X-ray; 3.20 A; A/D/G/J=1-295.
DR PDB; 6D3J; X-ray; 3.00 A; A=1-295.
DR PDB; 6D3M; X-ray; 2.03 A; A/B/F/J=1-295.
DR PDBsum; 6D0O; -.
DR PDBsum; 6D1O; -.
DR PDBsum; 6D3H; -.
DR PDBsum; 6D3I; -.
DR PDBsum; 6D3J; -.
DR PDBsum; 6D3M; -.
DR AlphaFoldDB; Q8KSC8; -.
DR SMR; Q8KSC8; -.
DR STRING; 76947.GCA_002080435_03094; -.
DR PRIDE; Q8KSC8; -.
DR BRENDA; 1.14.11.44; 13179.
DR UniPathway; UPA00348; -.
DR GO; GO:0051213; F:dioxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019439; P:aromatic compound catabolic process; 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; Aromatic hydrocarbons catabolism; Dioxygenase; Iron;
KW Metal-binding; Oxidoreductase.
FT CHAIN 1..295
FT /note="(R)-phenoxypropionate/alpha-ketoglutarate-
FT dioxygenase"
FT /id="PRO_0000430761"
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 SITE 221
FT /note="Contributes to enantiospecificity"
FT /evidence="ECO:0000303|PubMed:16731970"
FT SITE 285
FT /note="Contributes to enantiospecificity"
FT /evidence="ECO:0000303|PubMed:16731970"
FT MUTAGEN 80
FT /note="V->A: The dioxygenase activity with R-2,4-MCPP is
FT 60% of the wild-type. 6-fold decrease of the affinity
FT binding for R-2,4-MCPP."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 83
FT /note="L->A: The dioxygenase activity with R-2,4-MCPP is 5%
FT of the wild-type."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 93
FT /note="Q->A: The dioxygenase activity with R-2,4-MCPP is
FT 10% of the wild-type. 7-fold decrease of the affinity
FT binding for R-2,4-MCPP."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 106
FT /note="I->A: The dioxygenase activity with R-2,4-MCPP is
FT 30% of the wild-type. 20-fold decrease of the affinity
FT binding for R-2,4-MCPP. Loss of the dioxygenase activity;
FT when associated with I-107. The dioxygenase activity with
FT R-2,4-MCPP is 10% of the wild-type; when associated with N-
FT 107."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 107
FT /note="G->I: Loss of the dioxygenase activity; when
FT associated with A-106."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 107
FT /note="G->N: The dioxygenase activity with R-2,4-MCPP is
FT 10% of the wild-type; when associated with A-106."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 171
FT /note="F->A: The dioxygenase activity with R-2,4-MCPP is
FT 60% of the wild-type. 4-fold increase of the affinity
FT binding for R-2,4-MCPP."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 171
FT /note="F->Q: The dioxygenase activity with R-2,4-MCPP is
FT 60% of the wild-type and the affinity binding R-2,4-MCPP is
FT similar to the wild-type."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 221
FT /note="Y->A: The dioxygenase activity with R-2,4-MCPP is 5%
FT of the wild-type."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 285
FT /note="R->A: The dioxygenase activity with R-2,4-MCPP is
FT 10% of the wild-type. 4-fold decrease of the affinity
FT binding for R-2,4-MCPP."
FT /evidence="ECO:0000269|PubMed:16731970"
FT STRAND 13..24
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 26..30
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 39..52
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 53..59
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 64..72
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 89..97
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:6D1O"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:6D3H"
FT TURN 113..116
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 122..130
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 133..135
FT /evidence="ECO:0007829|PDB:6D3I"
FT STRAND 138..142
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 143..148
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 152..158
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 162..165
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 168..171
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 173..177
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 178..180
FT /evidence="ECO:0007829|PDB:6D3I"
FT TURN 184..186
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 192..196
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 199..206
FT /evidence="ECO:0007829|PDB:6D3H"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 213..215
FT /evidence="ECO:0007829|PDB:6D3H"
FT TURN 219..221
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 222..225
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 230..244
FT /evidence="ECO:0007829|PDB:6D3H"
FT HELIX 247..249
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 250..253
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 260..264
FT /evidence="ECO:0007829|PDB:6D3H"
FT TURN 265..267
FT /evidence="ECO:0007829|PDB:6D3H"
FT STRAND 268..272
FT /evidence="ECO:0007829|PDB:6D3H"
FT TURN 275..278
FT /evidence="ECO:0007829|PDB:6D3I"
FT STRAND 281..288
FT /evidence="ECO:0007829|PDB:6D3H"
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
