SDPA_SPHHM
ID SDPA_SPHHM Reviewed; 287 AA.
AC Q700X4;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 47.
DE RecName: Full=(S)-phenoxypropionate/alpha-ketoglutarate-dioxygenase {ECO:0000303|PubMed:15466552};
DE Short=SdpA {ECO:0000303|PubMed:15466552};
DE EC=1.14.11.43 {ECO:0000269|PubMed:16731970, ECO:0000269|PubMed:16820480};
DE AltName: Full=(S)-dichlorprop/(S)-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=sdpA {ECO:0000303|PubMed:15466552};
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=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 [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP COFACTOR, SUBSTRATE SPECIFICITY, AND PATHWAY.
RC STRAIN=ATCC 700291 / DSM 11019 / NBRC 16415 / MH;
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 [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF GLU-69; GLY-97; ASN-98; GLN-162; ARG-207; HIS-208 AND
RP HIS-272.
RC STRAIN=Strain MH;
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 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-chloro-2-
CC methylphenoxy)propionate ((RS)-2,4-MCPP) and phenoxyacetate derivatives
CC such as 2,4-dichlorophenoxyacetate (2,4-D), however it can only accept
CC 2-oxoglutarate as oxygen acceptor. {ECO:0000269|PubMed:16731970,
CC ECO:0000269|PubMed:16820480, ECO:0000303|PubMed:11423952}.
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|PubMed:16731970, ECO:0000269|PubMed:16820480};
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|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:0000269|PubMed:16820480};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=19.6 uM for alpha-ketoglutarate (at pH 6.75 and 30 degrees
CC Celsius)) {ECO:0000269|PubMed:16820480};
CC KM=132 uM for S-2,4-MCPP (at pH 6.75 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16820480};
CC KM=161 uM for S-2,4-MCPP (at pH 6.75 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16731970};
CC KM=234 uM for (RS)-2,4-MCPP (at pH 6.75 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16731970};
CC KM=494.8 uM for S-2,4-DP (at pH 6.75 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16820480};
CC Note=kcat is 229.7 min(-1) for dioxygenase activity with alpha-
CC ketoglutarate (at pH 6.75 and 30 degrees Celsius). kcat is 284.6
CC min(-1) for dioxygenase activity with S-2,4-DP (at pH 6.75 and 30
CC degrees Celsius). kcat is 303 min(-1) for dioxygenase activity with
CC S-2,4-MCPP (at pH 6.75 and 30 degrees Celsius). kcat is 899 min(-1)
CC for dioxygenase activity with (RS)-2,4-MCPP (at pH 6.75 and 30
CC degrees Celsius). kcat is 1010 min(-1) for dioxygenase activity with
CC S-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: Monomer. {ECO:0000269|PubMed:16820480}.
CC -!- SIMILARITY: Belongs to the TfdA dioxygenase family. {ECO:0000305}.
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DR EMBL; AJ628860; CAF32813.1; -; Genomic_DNA.
DR RefSeq; WP_037468461.1; NZ_JFZA02000051.1.
DR AlphaFoldDB; Q700X4; -.
DR SMR; Q700X4; -.
DR STRING; 1219045.BV98_003436; -.
DR eggNOG; COG2175; Bacteria.
DR OrthoDB; 1742732at2; -.
DR BRENDA; 1.14.11.43; 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 Aromatic hydrocarbons catabolism; Dioxygenase; Iron; Metal-binding;
KW Oxidoreductase.
FT CHAIN 1..287
FT /note="(S)-phenoxypropionate/alpha-ketoglutarate-
FT dioxygenase"
FT /id="PRO_0000430762"
FT BINDING 102
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 104
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 129
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 242
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 257
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT BINDING 268
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P37610"
FT SITE 69
FT /note="Contributes to enantiospecificity"
FT /evidence="ECO:0000303|PubMed:16731970"
FT SITE 207
FT /note="Contributes to enantiospecificity"
FT /evidence="ECO:0000303|PubMed:16731970"
FT MUTAGEN 69
FT /note="E->A: The dioxygenase activity with S-2,4-MCPP and
FT (RS)-2,4-MCPP is 30% and 20% of the wild-type,
FT respectively. Slight increase of the affinity binding for
FT S-2,4-MCPP and (RS)-2,4-MCPP."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 97
FT /note="G->I: The dioxygenase activity with S-2,4-MCPP and
FT (RS)-2,4-MCPP is strongly reduced and there is a 18-fold
FT decrease of the affinity binding for S-2,4-MCPP; when
FT associated with G-98."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 97
FT /note="G->N: Loss of the dioxygenase activity; when
FT associated with G-98."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 98
FT /note="N->G: The dioxygenase activity with S-2,4-MCPP and
FT (RS)-2,4-MCPP is strongly reduced; when associated with I-
FT 97. Loss of the dioxygenase activity; when associated with
FT N-97."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 162
FT /note="Q->F: The dioxygenase activity with S-2,4-MCPP and
FT (RS)-2,4-MCPP is strongly reduced."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 207
FT /note="R->A: The dioxygenase activity with S-2,4-MCPP and
FT (RS)-2,4-MCPP is 17 and 8% of the wild-type, respectively.
FT 15 and 10-fold decrease of the affinity binding for S-2,4-
FT MCPP and (RS)-2,4-MCPP, respectively."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 207
FT /note="R->V: The dioxygenase activity with S-2,4-MCPP and
FT (RS)-2,4-MCPP is strongly reduced."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 208
FT /note="H->A: The dioxygenase activity with S-2,4-MCPP and
FT (RS)-2,4-MCPP is strongly reduced. 18-fold decrease of the
FT affinity binding for R-2,4-MCPP."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 272
FT /note="H->A: The dioxygenase activity with S-2,4-MCPP and
FT (RS)-2,4-MCPP is strongly reduced."
FT /evidence="ECO:0000269|PubMed:16731970"
FT MUTAGEN 274
FT /note="R->A: Loss of the dioxygenase activity."
FT /evidence="ECO:0000269|PubMed:16731970"
SQ SEQUENCE 287 AA; 31746 MW; 0C827049F997D927 CRC64;
MSPAFDIAPL DATFGAVVTG VKLADLDDAG WLDLQAAWLE YALLVFPDQH LTREQQIAFA
RRFGPLEFEM AAISNVRPDG SLRVESDNDD MMKILKGNMG WHADSTYMPV QAKGAVFSAE
VVPSVGGQTG FADMRAAYDA LDEDLKARVE TLQARHSLHY SQSKLGHQTK AADGEYSGYG
LHDGPVPLRP LVKIHPETGR KSLLIGRHAH AIPGLEPAES ERLLQQLIDF ACQPPRIYHH
DWAPGDAVLW DNRCLLHQAT PWDMTQKRIM WHSRIAGDPA SETALAH
