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Protein

Biphenyl-2,3-diol 1,2-dioxygenase

Gene

bphC

Organism
Burkholderia xenovorans (strain LB400)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.

Catalytic activityi

Biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate.

Cofactori

Fe2+Note: Binds 1 Fe2+ ion per subunit.

Kineticsi

Substrate inhibition occurs at 300 µM (+/- 20 µM).

  1. KM=7 µM for biphenyl-2,3-diol

    pH dependencei

    Optimum pH is 8.0.

    Pathway: biphenyl degradation

    This protein is involved in step 3 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
    Metal bindingi146 – 1461Iron
    Metal bindingi210 – 2101Iron
    Metal bindingi260 – 2601Iron

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciBXEN266265:GJII-8843-MONOMER.
    SABIO-RKP47228.
    UniPathwayiUPA00155; UER00252.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Biphenyl-2,3-diol 1,2-dioxygenase (EC:1.13.11.39)
    Alternative name(s):
    2,3-dihydroxybiphenyl dioxygenase
    Short name:
    DHBD
    23OHBP oxygenase
    Gene namesi
    Name:bphC
    Ordered Locus Names:Bxeno_C1125
    ORF Names:Bxe_C1191
    OrganismiBurkholderia xenovorans (strain LB400)
    Taxonomic identifieri266265 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderia
    ProteomesiUP000001817 Componenti: Chromosome 3

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 298297Biphenyl-2,3-diol 1,2-dioxygenasePRO_0000085033Add
    BLAST

    Interactioni

    Subunit structurei

    Homooctamer. The enzyme is composed of two planar tetramers rotated at 45 degrees relative to each other, with a channel in the middle.1 Publication

    Protein-protein interaction databases

    STRINGi266265.Bxe_C1191.

    Structurei

    Secondary structure

    1
    298
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 1412Combined sources
    Helixi16 – 2510Combined sources
    Beta strandi30 – 356Combined sources
    Beta strandi38 – 4710Combined sources
    Beta strandi49 – 546Combined sources
    Beta strandi59 – 6911Combined sources
    Helixi70 – 8213Combined sources
    Helixi92 – 987Combined sources
    Beta strandi101 – 1077Combined sources
    Beta strandi113 – 1186Combined sources
    Beta strandi131 – 1333Combined sources
    Helixi140 – 1423Combined sources
    Beta strandi146 – 1505Combined sources
    Helixi154 – 16310Combined sources
    Beta strandi168 – 17811Combined sources
    Beta strandi181 – 19414Combined sources
    Beta strandi196 – 2005Combined sources
    Beta strandi205 – 21612Combined sources
    Helixi218 – 22912Combined sources
    Turni230 – 2323Combined sources
    Beta strandi234 – 24411Combined sources
    Beta strandi247 – 2526Combined sources
    Beta strandi258 – 2636Combined sources
    Beta strandi275 – 2784Combined sources
    Beta strandi280 – 2845Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HANX-ray1.90A2-298[»]
    1KMYX-ray2.00A2-298[»]
    1KNDX-ray1.90A2-298[»]
    1KNFX-ray1.90A2-298[»]
    1LGTX-ray1.70A2-298[»]
    1LKDX-ray1.70A2-298[»]
    ProteinModelPortaliP47228.
    SMRiP47228. Positions 2-289.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP47228.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0346.
    HOGENOMiHOG000052193.
    KOiK00462.
    OMAiGRHTNDH.
    OrthoDBiEOG64JFM4.

    Family and domain databases

    Gene3Di3.10.180.10. 2 hits.
    InterProiIPR017626. DiOHbiphenyl_dOase.
    IPR029068. Glyas_Bleomycin-R_OHBP_Dase.
    IPR004360. Glyas_Fos-R_dOase_dom.
    IPR000486. Xdiol_ring_cleave_dOase_1/2.
    [Graphical view]
    PfamiPF00903. Glyoxalase. 1 hit.
    [Graphical view]
    SUPFAMiSSF54593. SSF54593. 2 hits.
    TIGRFAMsiTIGR03213. 23dbph12diox. 1 hit.
    PROSITEiPS00082. EXTRADIOL_DIOXYGENAS. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P47228-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSIRSLGYMG FAVSDVAAWR SFLTQKLGLM EAGTTDNGDL FRIDSRAWRI
    60 70 80 90 100
    AVQQGEVDDL AFAGYEVADA AGLAQMADKL KQAGIAVTTG DASLARRRGV
    110 120 130 140 150
    TGLITFADPF GLPLEIYYGA SEVFEKPFLP GAAVSGFLTG EQGLGHFVRC
    160 170 180 190 200
    VPDSDKALAF YTDVLGFQLS DVIDMKMGPD VTVPAYFLHC NERHHTLAIA
    210 220 230 240 250
    AFPLPKRIHH FMLEVASLDD VGFAFDRVDA DGLITSTLGR HTNDHMVSFY
    260 270 280 290
    ASTPSGVEVE YGWSARTVDR SWVVVRHDSP SMWGHKSVRD KAAARNKA
    Length:298
    Mass (Da):32,471
    Last modified:January 23, 2007 - v2
    Checksum:iADC0E4709E193FAB
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X66122 Genomic DNA. Translation: CAA46910.1.
    CP000272 Genomic DNA. Translation: ABE37053.1.
    PIRiJN0815.
    RefSeqiWP_011494295.1. NC_007953.1.
    YP_556403.1. NC_007953.1.

    Genome annotation databases

    EnsemblBacteriaiABE37053; ABE37053; Bxe_C1191.
    KEGGibxe:Bxe_C1191.
    PATRICi19343367. VBIBurXen52548_8941.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X66122 Genomic DNA. Translation: CAA46910.1.
    CP000272 Genomic DNA. Translation: ABE37053.1.
    PIRiJN0815.
    RefSeqiWP_011494295.1. NC_007953.1.
    YP_556403.1. NC_007953.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HANX-ray1.90A2-298[»]
    1KMYX-ray2.00A2-298[»]
    1KNDX-ray1.90A2-298[»]
    1KNFX-ray1.90A2-298[»]
    1LGTX-ray1.70A2-298[»]
    1LKDX-ray1.70A2-298[»]
    ProteinModelPortaliP47228.
    SMRiP47228. Positions 2-289.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi266265.Bxe_C1191.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiABE37053; ABE37053; Bxe_C1191.
    KEGGibxe:Bxe_C1191.
    PATRICi19343367. VBIBurXen52548_8941.

    Phylogenomic databases

    eggNOGiCOG0346.
    HOGENOMiHOG000052193.
    KOiK00462.
    OMAiGRHTNDH.
    OrthoDBiEOG64JFM4.

    Enzyme and pathway databases

    UniPathwayiUPA00155; UER00252.
    BioCyciBXEN266265:GJII-8843-MONOMER.
    SABIO-RKP47228.

    Miscellaneous databases

    EvolutionaryTraceiP47228.

    Family and domain databases

    Gene3Di3.10.180.10. 2 hits.
    InterProiIPR017626. DiOHbiphenyl_dOase.
    IPR029068. Glyas_Bleomycin-R_OHBP_Dase.
    IPR004360. Glyas_Fos-R_dOase_dom.
    IPR000486. Xdiol_ring_cleave_dOase_1/2.
    [Graphical view]
    PfamiPF00903. Glyoxalase. 1 hit.
    [Graphical view]
    SUPFAMiSSF54593. SSF54593. 2 hits.
    TIGRFAMsiTIGR03213. 23dbph12diox. 1 hit.
    PROSITEiPS00082. EXTRADIOL_DIOXYGENAS. 1 hit.
    [Graphical view]
    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. "Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase."
      Eltis L.D., Hofmann B., Hecht H.J., Luensdorf H., Timmis K.N.
      J. Biol. Chem. 268:2727-2732(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-32, SUBSTRATE CHARACTERIZATION, PRELIMINARY CRYSTALLIZATION, SUBUNIT.
    4. "Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad."
      Han S., Eltis L.D., Timmis K.N., Muchmore S.W., Bolin J.T.
      Science 270:976-980(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
    5. "Molecular basis for the stabilization and inhibition of 2,3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol."
      Vaillancourt F.H., Han S., Fortin P.D., Bolin J.T., Eltis L.D.
      J. Biol. Chem. 273:34887-34895(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).

    Entry informationi

    Entry nameiBPHC_BURXL
    AccessioniPrimary (citable) accession number: P47228
    Secondary accession number(s): Q13FT6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: January 23, 2007
    Last modified: April 1, 2015
    This is version 116 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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

    External Data

    Dasty 3

    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 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.