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Protein

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

Gene

bphD

Organism
Paraburkholderia xenovorans (strain LB400)
Status
Reviewed-Annotation score: -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.

Activity 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 beta (bphE), Biphenyl dioxygenase subunit alpha (bphA)
    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)DescriptionActionsGraphical viewLength
    Binding sitei51Substrate1
    Binding sitei111Substrate1
    Sitei112Transition state stabilizer1
    Binding sitei180Substrate; via carbonyl oxygen1
    Binding sitei190Substrate1
    Active sitei265Proton acceptor1
    Binding sitei266Substrate1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionHydrolase
    Biological processAromatic hydrocarbons catabolism

    Enzyme and pathway databases

    BRENDAi3.7.1.8 7691
    SABIO-RKiP47229
    UniPathwayi
    UPA00155;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
    OrganismiParaburkholderia xenovorans (strain LB400)
    Taxonomic identifieri266265 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
    Proteomesi
    • UP000001817 Componenti: Chromosome 3

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi112S → A: Catalyzes the tautomerisation of HOPDA. Extremely low hydrolase activity; when associated with A-265. 1 Publication1
    Mutagenesisi265H → A: Unable to catalyze the tautomerisation of HOPDA. Extremely low hydrolase activity; when associated with A-112. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002070521 – 2862-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolaseAdd BLAST286

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi266265.Bxe_C1186

    Structurei

    Secondary structure

    1286
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliP47229
    SMRiP47229
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP47229

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni42 – 43Substrate binding2

    Sequence similaritiesi

    Belongs to the AB hydrolase superfamily. BphD family.Curated

    Phylogenomic databases

    eggNOGiENOG4106HB6 Bacteria
    COG0596 LUCA
    HOGENOMiHOG000028063
    KOiK10222
    OMAiKCGHWAQ
    OrthoDBiPOG091H05R7

    Family and domain databases

    Gene3Di3.40.50.1820, 1 hit
    HAMAPiMF_01688 Biphenyl_BphD, 1 hit
    InterProiView protein in InterPro
    IPR029058 AB_hydrolase
    IPR000073 AB_hydrolase_1
    IPR000639 Epox_hydrolase-like
    IPR017727 HOPD_hydrolase_BphD
    PfamiView protein in Pfam
    PF12697 Abhydrolase_6, 1 hit
    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

    Similar proteinsi

    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
    PDB 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
    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

    Phylogenomic databases

    eggNOGiENOG4106HB6 Bacteria
    COG0596 LUCA
    HOGENOMiHOG000028063
    KOiK10222
    OMAiKCGHWAQ
    OrthoDBiPOG091H05R7

    Enzyme and pathway databases

    UniPathwayi
    UPA00155;UER00253

    BRENDAi3.7.1.8 7691
    SABIO-RKiP47229

    Miscellaneous databases

    EvolutionaryTraceiP47229

    Family and domain databases

    Gene3Di3.40.50.1820, 1 hit
    HAMAPiMF_01688 Biphenyl_BphD, 1 hit
    InterProiView protein in InterPro
    IPR029058 AB_hydrolase
    IPR000073 AB_hydrolase_1
    IPR000639 Epox_hydrolase-like
    IPR017727 HOPD_hydrolase_BphD
    PfamiView protein in Pfam
    PF12697 Abhydrolase_6, 1 hit
    PRINTSiPR00111 ABHYDROLASE
    PR00412 EPOXHYDRLASE
    SUPFAMiSSF53474 SSF53474, 1 hit
    TIGRFAMsiTIGR03343 biphenyl_bphD, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiBPHD_PARXL
    AccessioniPrimary (citable) accession number: P47229
    Secondary accession number(s): Q13FU1
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: February 1, 1996
    Last modified: November 7, 2018
    This is version 122 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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