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Protein

2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase

Gene

bphD

Organism
Burkholderia xenovorans (strain LB400)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD).1 Publication

Catalytic activityi

2,6-dioxo-6-phenylhexa-3-enoate + H2O = benzoate + 2-oxopent-4-enoate.

Enzyme regulationi

Inhibited by 3-Cl HOPDA.

Kineticsi

  1. KM=0.2 µM for HOPDA1 Publication
  2. KM=0.54 µM for 3-Cl HOPDA1 Publication
  3. KM=4.8 µM for 3-F HOPDA1 Publication

    Pathwayi: biphenyl degradation

    This protein is involved in step 4 of the subpathway that synthesizes 2-hydroxy-2,4-pentadienoate and benzoate from biphenyl.
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. Biphenyl dioxygenase subunit alpha (bphA), Biphenyl dioxygenase subunit beta (bphE)
    2. Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (bphB)
    3. Biphenyl-2,3-diol 1,2-dioxygenase (bphC)
    4. 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (bphD)
    This subpathway is part of the pathway biphenyl degradation, which is itself part of Xenobiotic degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2-hydroxy-2,4-pentadienoate and benzoate from biphenyl, the pathway biphenyl degradation and in Xenobiotic degradation.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei51 – 511Substrate
    Binding sitei111 – 1111Substrate
    Sitei112 – 1121Transition state stabilizer
    Binding sitei180 – 1801Substrate; via carbonyl oxygen
    Binding sitei190 – 1901Substrate
    Active sitei265 – 2651Proton acceptor
    Binding sitei266 – 2661Substrate

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism

    Enzyme and pathway databases

    BioCyciBXEN266265:GJII-8838-MONOMER.
    BRENDAi3.7.1.8. 7691.
    SABIO-RKP47229.
    UniPathwayiUPA00155; UER00253.

    Protein family/group databases

    ESTHERiburxl-bphD. Carbon-carbon_bond_hydrolase.
    MEROPSiS33.016.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC:3.7.1.8)
    Short name:
    HOPDA hydrolase
    Alternative name(s):
    2,6-dioxo-6-phenylhexa-3-enoate hydrolase
    Gene namesi
    Name:bphD
    Ordered Locus Names:Bxeno_C1120
    ORF Names:Bxe_C1186
    OrganismiBurkholderia xenovorans (strain LB400)
    Taxonomic identifieri266265 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
    Proteomesi
    • UP000001817 Componenti: Chromosome 3

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi112 – 1121S → A: Catalyzes the tautomerisation of HOPDA. Extremely low hydrolase activity; when associated with A-265. 1 Publication
    Mutagenesisi265 – 2651H → A: Unable to catalyze the tautomerisation of HOPDA. Extremely low hydrolase activity; when associated with A-112. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2862862-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolasePRO_0000207052Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi266265.Bxe_C1186.

    Structurei

    Secondary structure

    1
    286
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 94Combined sources
    Beta strandi10 – 156Combined sources
    Beta strandi17 – 193Combined sources
    Beta strandi21 – 3010Combined sources
    Beta strandi33 – 397Combined sources
    Helixi48 – 525Combined sources
    Turni53 – 553Combined sources
    Helixi56 – 616Combined sources
    Beta strandi65 – 695Combined sources
    Helixi86 – 10015Combined sources
    Beta strandi106 – 1116Combined sources
    Helixi113 – 12412Combined sources
    Helixi126 – 1283Combined sources
    Beta strandi129 – 1368Combined sources
    Beta strandi144 – 1463Combined sources
    Helixi151 – 16111Combined sources
    Helixi165 – 17511Combined sources
    Helixi179 – 1813Combined sources
    Helixi184 – 19613Combined sources
    Helixi198 – 21013Combined sources
    Helixi213 – 2164Combined sources
    Helixi219 – 2246Combined sources
    Beta strandi229 – 2346Combined sources
    Beta strandi238 – 2403Combined sources
    Helixi243 – 2519Combined sources
    Beta strandi252 – 26211Combined sources
    Helixi267 – 2704Combined sources
    Helixi272 – 28514Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2OG1X-ray1.60A/B1-286[»]
    2PU5X-ray2.30A/B1-286[»]
    2PU7X-ray2.07A1-286[»]
    2PUHX-ray1.82A1-286[»]
    2PUJX-ray1.57A1-286[»]
    2RHTX-ray1.70A4-286[»]
    2RHWX-ray1.57A4-286[»]
    2RI6X-ray1.68A4-286[»]
    3V1KX-ray2.13A/B1-286[»]
    3V1LX-ray2.11A1-286[»]
    3V1MX-ray1.92A1-286[»]
    3V1NX-ray1.59A1-286[»]
    ProteinModelPortaliP47229.
    SMRiP47229. Positions 2-286.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP47229.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni42 – 432Substrate binding

    Sequence similaritiesi

    Belongs to the AB hydrolase superfamily. BphD family.Curated

    Phylogenomic databases

    eggNOGiENOG4106HB6. Bacteria.
    COG0596. LUCA.
    HOGENOMiHOG000028063.
    KOiK10222.
    OMAiWFAYDES.
    OrthoDBiEOG6PS5TK.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    HAMAPiMF_01688. Biphenyl_BphD.
    InterProiIPR029058. AB_hydrolase.
    IPR000073. AB_hydrolase_1.
    IPR000639. Epox_hydrolase-like.
    IPR017727. HOPD_hydrolase_BphD.
    [Graphical view]
    PfamiPF12697. Abhydrolase_6. 1 hit.
    [Graphical view]
    PRINTSiPR00111. ABHYDROLASE.
    PR00412. EPOXHYDRLASE.
    SUPFAMiSSF53474. SSF53474. 1 hit.
    TIGRFAMsiTIGR03343. biphenyl_bphD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P47229-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTALTESSTS KFVKINEKGF SDFNIHYNEA GNGETVIMLH GGGPGAGGWS
    60 70 80 90 100
    NYYRNVGPFV DAGYRVILKD SPGFNKSDAV VMDEQRGLVN ARAVKGLMDA
    110 120 130 140 150
    LDIDRAHLVG NSMGGATALN FALEYPDRIG KLILMGPGGL GPSMFAPMPM
    160 170 180 190 200
    EGIKLLFKLY AEPSYETLKQ MLQVFLYDQS LITEELLQGR WEAIQRQPEH
    210 220 230 240 250
    LKNFLISAQK APLSTWDVTA RLGEIKAKTF ITWGRDDRFV PLDHGLKLLW
    260 270 280
    NIDDARLHVF SKCGHWAQWE HADEFNRLVI DFLRHA
    Length:286
    Mass (Da):32,030
    Last modified:February 1, 1996 - v1
    Checksum:i1E41575C172F5A0C
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X66123 Genomic DNA. Translation: CAA46911.1.
    CP000272 Genomic DNA. Translation: ABE37048.1.
    RefSeqiWP_011494293.1. NZ_CP008761.1.

    Genome annotation databases

    EnsemblBacteriaiABE37048; ABE37048; Bxe_C1186.
    GeneIDi4010698.
    KEGGibxb:DR64_8619.
    bxe:Bxe_C1186.
    PATRICi19343357. VBIBurXen52548_8936.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X66123 Genomic DNA. Translation: CAA46911.1.
    CP000272 Genomic DNA. Translation: ABE37048.1.
    RefSeqiWP_011494293.1. NZ_CP008761.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2OG1X-ray1.60A/B1-286[»]
    2PU5X-ray2.30A/B1-286[»]
    2PU7X-ray2.07A1-286[»]
    2PUHX-ray1.82A1-286[»]
    2PUJX-ray1.57A1-286[»]
    2RHTX-ray1.70A4-286[»]
    2RHWX-ray1.57A4-286[»]
    2RI6X-ray1.68A4-286[»]
    3V1KX-ray2.13A/B1-286[»]
    3V1LX-ray2.11A1-286[»]
    3V1MX-ray1.92A1-286[»]
    3V1NX-ray1.59A1-286[»]
    ProteinModelPortaliP47229.
    SMRiP47229. Positions 2-286.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi266265.Bxe_C1186.

    Protein family/group databases

    ESTHERiburxl-bphD. Carbon-carbon_bond_hydrolase.
    MEROPSiS33.016.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiABE37048; ABE37048; Bxe_C1186.
    GeneIDi4010698.
    KEGGibxb:DR64_8619.
    bxe:Bxe_C1186.
    PATRICi19343357. VBIBurXen52548_8936.

    Phylogenomic databases

    eggNOGiENOG4106HB6. Bacteria.
    COG0596. LUCA.
    HOGENOMiHOG000028063.
    KOiK10222.
    OMAiWFAYDES.
    OrthoDBiEOG6PS5TK.

    Enzyme and pathway databases

    UniPathwayiUPA00155; UER00253.
    BioCyciBXEN266265:GJII-8838-MONOMER.
    BRENDAi3.7.1.8. 7691.
    SABIO-RKP47229.

    Miscellaneous databases

    EvolutionaryTraceiP47229.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    HAMAPiMF_01688. Biphenyl_BphD.
    InterProiIPR029058. AB_hydrolase.
    IPR000073. AB_hydrolase_1.
    IPR000639. Epox_hydrolase-like.
    IPR017727. HOPD_hydrolase_BphD.
    [Graphical view]
    PfamiPF12697. Abhydrolase_6. 1 hit.
    [Graphical view]
    PRINTSiPR00111. ABHYDROLASE.
    PR00412. EPOXHYDRLASE.
    SUPFAMiSSF53474. SSF53474. 1 hit.
    TIGRFAMsiTIGR03343. biphenyl_bphD. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Genetic analysis of a Pseudomonas locus encoding a pathway for biphenyl/polychlorinated biphenyl degradation."
      Hofer B., Eltis L.D., Dowling D.N., Timmis K.N.
      Gene 130:47-55(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LB400.
    3. "Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway."
      Horsman G.P., Ke J., Dai S., Seah S.Y.K., Bolin J.T., Eltis L.D.
      Biochemistry 45:11071-11086(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF MUTANT ALA-112 IN COMPLEXES WITH ANALOGS SUBSTRATE, FUNCTION, SUBUNIT.
    4. "The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad."
      Horsman G.P., Bhowmik S., Seah S.Y., Kumar P., Bolin J.T., Eltis L.D.
      J. Biol. Chem. 282:19894-19904(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT ALA-112 AND ALA-112/ALA-265 IN COMPLEXES WITH ANALOGS SUBSTRATE, MUTAGENESIS OF SER-112 AND HIS-265, REACTION MECHANISM.
    5. "The molecular basis for inhibition of BphD, a C-C bond hydrolase involved in polychlorinated biphenyls degradation: large 3-substituents prevent tautomerization."
      Bhowmik S., Horsman G.P., Bolin J.T., Eltis L.D.
      J. Biol. Chem. 282:36377-36385(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 4-286 MUTANT ALA-112 IN COMPLEXES WITH ANALOGS SUBSTRATE, BIOPHYSICOCHEMICAL PROPERTIES, INHIBITORS.

    Entry informationi

    Entry nameiBPHD_BURXL
    AccessioniPrimary (citable) accession number: P47229
    Secondary accession number(s): Q13FU1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: February 1, 1996
    Last modified: June 8, 2016
    This is version 111 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.