Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)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

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism

    Enzyme and pathway databases

    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)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
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 9Combined sources4
    Beta strandi10 – 15Combined sources6
    Beta strandi17 – 19Combined sources3
    Beta strandi21 – 30Combined sources10
    Beta strandi33 – 39Combined sources7
    Helixi48 – 52Combined sources5
    Turni53 – 55Combined sources3
    Helixi56 – 61Combined sources6
    Beta strandi65 – 69Combined sources5
    Helixi86 – 100Combined sources15
    Beta strandi106 – 111Combined sources6
    Helixi113 – 124Combined sources12
    Helixi126 – 128Combined sources3
    Beta strandi129 – 136Combined sources8
    Beta strandi144 – 146Combined sources3
    Helixi151 – 161Combined sources11
    Helixi165 – 175Combined sources11
    Helixi179 – 181Combined sources3
    Helixi184 – 196Combined sources13
    Helixi198 – 210Combined sources13
    Helixi213 – 216Combined sources4
    Helixi219 – 224Combined sources6
    Beta strandi229 – 234Combined sources6
    Beta strandi238 – 240Combined sources3
    Helixi243 – 251Combined sources9
    Beta strandi252 – 262Combined sources11
    Helixi267 – 270Combined sources4
    Helixi272 – 285Combined sources14

    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...

    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.
    OMAiWFAYDES.
    OrthoDBiPOG091H05R7.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    HAMAPiMF_01688. Biphenyl_BphD. 1 hit.
    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
    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.
    PATRICi19343357. VBIBurXen52548_8936.

    Phylogenomic databases

    eggNOGiENOG4106HB6. Bacteria.
    COG0596. LUCA.
    HOGENOMiHOG000028063.
    KOiK10222.
    OMAiWFAYDES.
    OrthoDBiPOG091H05R7.

    Enzyme and pathway databases

    UniPathwayiUPA00155; UER00253.
    BRENDAi3.7.1.8. 7691.
    SABIO-RKP47229.

    Miscellaneous databases

    EvolutionaryTraceiP47229.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    HAMAPiMF_01688. Biphenyl_BphD. 1 hit.
    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...

    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: November 2, 2016
    This is version 114 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.