BPHD_PARXL
ID BPHD_PARXL Reviewed; 286 AA.
AC P47229; Q13FU1;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase;
DE Short=HOPDA hydrolase;
DE EC=3.7.1.8;
DE AltName: Full=2,6-dioxo-6-phenylhexa-3-enoate hydrolase;
GN Name=bphD; OrderedLocusNames=Bxeno_C1120; ORFNames=Bxe_C1186;
OS Paraburkholderia xenovorans (strain LB400).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Paraburkholderia.
OX NCBI_TaxID=266265;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8344527; DOI=10.1016/0378-1119(93)90345-4;
RA Hofer B., Eltis L.D., Dowling D.N., Timmis K.N.;
RT "Genetic analysis of a Pseudomonas locus encoding a pathway for
RT biphenyl/polychlorinated biphenyl degradation.";
RL Gene 130:47-55(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LB400;
RX PubMed=17030797; DOI=10.1073/pnas.0606924103;
RA Chain P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L.,
RA Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V.,
RA Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J.,
RA Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T.,
RA Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M.;
RT "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome
RT shaped for versatility.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF MUTANT ALA-112 IN COMPLEXES WITH
RP ANALOGS SUBSTRATE, FUNCTION, AND SUBUNIT.
RX PubMed=16964968; DOI=10.1021/bi0611098;
RA Horsman G.P., Ke J., Dai S., Seah S.Y.K., Bolin J.T., Eltis L.D.;
RT "Kinetic and structural insight into the mechanism of BphD, a C-C bond
RT hydrolase from the biphenyl degradation pathway.";
RL Biochemistry 45:11071-11086(2006).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT ALA-112 AND ALA-112/ALA-265
RP IN COMPLEXES WITH ANALOGS SUBSTRATE, MUTAGENESIS OF SER-112 AND HIS-265,
RP AND REACTION MECHANISM.
RX PubMed=17442675; DOI=10.1074/jbc.m702237200;
RA Horsman G.P., Bhowmik S., Seah S.Y., Kumar P., Bolin J.T., Eltis L.D.;
RT "The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and
RT structural evidence supporting a key role for histidine 265 of the
RT catalytic triad.";
RL J. Biol. Chem. 282:19894-19904(2007).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 4-286 MUTANT ALA-112 IN COMPLEXES
RP WITH ANALOGS SUBSTRATE, BIOPHYSICOCHEMICAL PROPERTIES, AND INHIBITORS.
RX PubMed=17932031; DOI=10.1074/jbc.m707035200;
RA Bhowmik S., Horsman G.P., Bolin J.T., Eltis L.D.;
RT "The molecular basis for inhibition of BphD, a C-C bond hydrolase involved
RT in polychlorinated biphenyls degradation: large 3-substituents prevent
RT tautomerization.";
RL J. Biol. Chem. 282:36377-36385(2007).
CC -!- FUNCTION: Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-
CC 6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2-
CC hydroxy-2,4-pentadienoic acid (HPD). {ECO:0000269|PubMed:16964968}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,6-dioxo-6-phenylhexa-3-enoate + H2O = 2-oxopent-4-enoate +
CC benzoate + H(+); Xref=Rhea:RHEA:17161, ChEBI:CHEBI:11641,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16150,
CC ChEBI:CHEBI:64675; EC=3.7.1.8;
CC -!- ACTIVITY REGULATION: Inhibited by 3-Cl HOPDA.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.2 uM for HOPDA {ECO:0000269|PubMed:17932031};
CC KM=0.54 uM for 3-Cl HOPDA {ECO:0000269|PubMed:17932031};
CC KM=4.8 uM for 3-F HOPDA {ECO:0000269|PubMed:17932031};
CC -!- PATHWAY: Xenobiotic degradation; biphenyl degradation; 2-hydroxy-2,4-
CC pentadienoate and benzoate from biphenyl: step 4/4.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16964968}.
CC -!- SIMILARITY: Belongs to the AB hydrolase superfamily. BphD family.
CC {ECO:0000305}.
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DR EMBL; X66123; CAA46911.1; -; Genomic_DNA.
DR EMBL; CP000272; ABE37048.1; -; Genomic_DNA.
DR RefSeq; WP_011494293.1; NZ_CP008761.1.
DR PDB; 2OG1; X-ray; 1.60 A; A/B=1-286.
DR PDB; 2PU5; X-ray; 2.30 A; A/B=1-286.
DR PDB; 2PU7; X-ray; 2.07 A; A=1-286.
DR PDB; 2PUH; X-ray; 1.82 A; A=1-286.
DR PDB; 2PUJ; X-ray; 1.57 A; A=1-286.
DR PDB; 2RHT; X-ray; 1.70 A; A=4-286.
DR PDB; 2RHW; X-ray; 1.57 A; A=4-286.
DR PDB; 2RI6; X-ray; 1.68 A; A=4-286.
DR PDB; 3V1K; X-ray; 2.13 A; A/B=1-286.
DR PDB; 3V1L; X-ray; 2.11 A; A=1-286.
DR PDB; 3V1M; X-ray; 1.92 A; A=1-286.
DR PDB; 3V1N; X-ray; 1.59 A; A=1-286.
DR PDBsum; 2OG1; -.
DR PDBsum; 2PU5; -.
DR PDBsum; 2PU7; -.
DR PDBsum; 2PUH; -.
DR PDBsum; 2PUJ; -.
DR PDBsum; 2RHT; -.
DR PDBsum; 2RHW; -.
DR PDBsum; 2RI6; -.
DR PDBsum; 3V1K; -.
DR PDBsum; 3V1L; -.
DR PDBsum; 3V1M; -.
DR PDBsum; 3V1N; -.
DR AlphaFoldDB; P47229; -.
DR SMR; P47229; -.
DR STRING; 266265.Bxe_C1186; -.
DR DrugBank; DB07915; (2E,4E)-2-Hydroxy-6-oxo-6-phenyl-2,4-hexadienoic acid.
DR DrugBank; DB07516; (2Z,4E)-3-chloro-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid.
DR DrugBank; DB07911; (3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE.
DR DrugBank; DB07510; 3-fluoro-6-(4-fluorophenyl)-2-hydroxy-6-oxohexa-2,4-dienoic acid.
DR ESTHER; burxl-bphD; Carbon-carbon_bond_hydrolase.
DR MEROPS; S33.016; -.
DR EnsemblBacteria; ABE37048; ABE37048; Bxe_C1186.
DR KEGG; bxb:DR64_8619; -.
DR KEGG; bxe:Bxe_C1186; -.
DR eggNOG; COG0596; Bacteria.
DR OMA; YWAMMHK; -.
DR OrthoDB; 1119700at2; -.
DR BRENDA; 3.7.1.8; 7691.
DR SABIO-RK; P47229; -.
DR UniPathway; UPA00155; UER00253.
DR EvolutionaryTrace; P47229; -.
DR Proteomes; UP000001817; Chromosome 3.
DR GO; GO:0018774; F:2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity; IEA:UniProtKB-EC.
DR GO; GO:0018771; F:2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0019439; P:aromatic compound catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.1820; -; 1.
DR HAMAP; MF_01688; Biphenyl_BphD; 1.
DR InterPro; IPR029058; AB_hydrolase.
DR InterPro; IPR000073; AB_hydrolase_1.
DR InterPro; IPR000639; Epox_hydrolase-like.
DR InterPro; IPR017727; HOPD_hydrolase_BphD.
DR Pfam; PF12697; Abhydrolase_6; 1.
DR PRINTS; PR00111; ABHYDROLASE.
DR PRINTS; PR00412; EPOXHYDRLASE.
DR SUPFAM; SSF53474; SSF53474; 1.
DR TIGRFAMs; TIGR03343; biphenyl_bphD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aromatic hydrocarbons catabolism; Hydrolase;
KW Reference proteome.
FT CHAIN 1..286
FT /note="2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase"
FT /id="PRO_0000207052"
FT ACT_SITE 265
FT /note="Proton acceptor"
FT BINDING 42..43
FT /ligand="substrate"
FT BINDING 51
FT /ligand="substrate"
FT BINDING 111
FT /ligand="substrate"
FT BINDING 180
FT /ligand="substrate"
FT BINDING 190
FT /ligand="substrate"
FT BINDING 266
FT /ligand="substrate"
FT SITE 112
FT /note="Transition state stabilizer"
FT MUTAGEN 112
FT /note="S->A: Catalyzes the tautomerisation of HOPDA.
FT Extremely low hydrolase activity; when associated with A-
FT 265."
FT /evidence="ECO:0000269|PubMed:17442675"
FT MUTAGEN 265
FT /note="H->A: Unable to catalyze the tautomerisation of
FT HOPDA. Extremely low hydrolase activity; when associated
FT with A-112."
FT /evidence="ECO:0000269|PubMed:17442675"
FT HELIX 6..9
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 10..15
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 17..19
FT /evidence="ECO:0007829|PDB:2PU7"
FT STRAND 21..30
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 33..39
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 48..52
FT /evidence="ECO:0007829|PDB:2PUJ"
FT TURN 53..55
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 56..61
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 65..69
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 86..100
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 113..124
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 129..136
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 151..161
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 165..175
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 184..196
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 198..210
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 213..216
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 219..224
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 229..234
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 243..251
FT /evidence="ECO:0007829|PDB:2PUJ"
FT STRAND 252..262
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 267..270
FT /evidence="ECO:0007829|PDB:2PUJ"
FT HELIX 272..285
FT /evidence="ECO:0007829|PDB:2PUJ"
SQ SEQUENCE 286 AA; 32030 MW; 1E41575C172F5A0C CRC64;
MTALTESSTS KFVKINEKGF SDFNIHYNEA GNGETVIMLH GGGPGAGGWS NYYRNVGPFV
DAGYRVILKD SPGFNKSDAV VMDEQRGLVN ARAVKGLMDA LDIDRAHLVG NSMGGATALN
FALEYPDRIG KLILMGPGGL GPSMFAPMPM EGIKLLFKLY AEPSYETLKQ MLQVFLYDQS
LITEELLQGR WEAIQRQPEH LKNFLISAQK APLSTWDVTA RLGEIKAKTF ITWGRDDRFV
PLDHGLKLLW NIDDARLHVF SKCGHWAQWE HADEFNRLVI DFLRHA
