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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.

    Pathwayi: 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)DescriptionActionsGraphical viewLength
    Metal bindingi146Iron1
    Metal bindingi210Iron1
    Metal bindingi260Iron1

    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

    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 lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
    Proteomesi
    • UP000001817 Componenti: Chromosome 3

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00000850332 – 298Biphenyl-2,3-diol 1,2-dioxygenaseAdd BLAST297

    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

    1298
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 14Combined sources12
    Helixi16 – 25Combined sources10
    Beta strandi30 – 35Combined sources6
    Beta strandi38 – 47Combined sources10
    Beta strandi49 – 54Combined sources6
    Beta strandi59 – 69Combined sources11
    Helixi70 – 82Combined sources13
    Helixi92 – 98Combined sources7
    Beta strandi101 – 107Combined sources7
    Beta strandi113 – 118Combined sources6
    Beta strandi131 – 133Combined sources3
    Helixi140 – 142Combined sources3
    Beta strandi146 – 150Combined sources5
    Helixi154 – 163Combined sources10
    Beta strandi168 – 178Combined sources11
    Beta strandi181 – 194Combined sources14
    Beta strandi196 – 200Combined sources5
    Beta strandi205 – 216Combined sources12
    Helixi218 – 229Combined sources12
    Turni230 – 232Combined sources3
    Beta strandi234 – 244Combined sources11
    Beta strandi247 – 252Combined sources6
    Beta strandi258 – 263Combined sources6
    Beta strandi275 – 278Combined sources4
    Beta strandi280 – 284Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP47228.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105H37. Bacteria.
    COG0346. LUCA.
    HOGENOMiHOG000052193.
    KOiK00462.
    OMAiGRHTNDH.
    OrthoDBiPOG091H0B2E.

    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.

    Genome annotation databases

    EnsemblBacteriaiABE37053; ABE37053; Bxe_C1191.
    KEGGibxb:DR64_8614.
    bxe: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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi266265.Bxe_C1191.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiABE37053; ABE37053; Bxe_C1191.
    KEGGibxb:DR64_8614.
    bxe:Bxe_C1191.
    PATRICi19343367. VBIBurXen52548_8941.

    Phylogenomic databases

    eggNOGiENOG4105H37. Bacteria.
    COG0346. LUCA.
    HOGENOMiHOG000052193.
    KOiK00462.
    OMAiGRHTNDH.
    OrthoDBiPOG091H0B2E.

    Enzyme and pathway databases

    UniPathwayiUPA00155; UER00252.
    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...

    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: November 2, 2016
    This is version 124 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

    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.