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Protein

Biphenyl dioxygenase subunit alpha

Gene

bphA

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

Functioni

Catalytic activityi

Biphenyl + NADH + O2 = (1S,2R)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+.

Cofactori

Protein has several cofactor binding sites:

Pathwayi: biphenyl degradation

This protein is involved in step 1 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 bindingi100 – 1001Iron-sulfur (2Fe-2S)PROSITE-ProRule annotation
Metal bindingi102 – 1021Iron-sulfur (2Fe-2S); via pros nitrogenPROSITE-ProRule annotation
Metal bindingi120 – 1201Iron-sulfur (2Fe-2S)PROSITE-ProRule annotation
Metal bindingi123 – 1231Iron-sulfur (2Fe-2S); via pros nitrogenPROSITE-ProRule annotation
Metal bindingi233 – 2331IronBy similarity
Metal bindingi239 – 2391IronBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

Aromatic hydrocarbons catabolism

Keywords - Ligandi

2Fe-2S, Iron, Iron-sulfur, Metal-binding, NAD

Enzyme and pathway databases

BioCyciBXEN266265:GJII-8849-MONOMER.
BRENDAi1.14.12.18. 7691.
UniPathwayiUPA00155; UER00250.

Names & Taxonomyi

Protein namesi
Recommended name:
Biphenyl dioxygenase subunit alpha (EC:1.14.12.18)
Alternative name(s):
Biphenyl 2,3-dioxygenase
Gene namesi
Name:bphA
Ordered Locus Names:Bxeno_C1131
ORF Names:Bxe_C1197
OrganismiBurkholderia xenovorans (strain LB400)
Taxonomic identifieri266265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderia
Proteomesi
  • UP000001817 Componenti: Chromosome 3

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 459458Biphenyl dioxygenase subunit alphaPRO_0000085046Add
BLAST

Interactioni

Subunit structurei

Heterohexamer consisting of three BphA subunits and three BphE subunits. A ferredoxin (BphF) and a ferredoxin reductase (BphG) must be present to obtain activity.

Protein-protein interaction databases

STRINGi266265.Bxe_C1197.

Structurei

Secondary structure

1
459
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 255Combined sources
Turni30 – 334Combined sources
Helixi37 – 404Combined sources
Helixi43 – 5210Combined sources
Turni53 – 564Combined sources
Beta strandi59 – 635Combined sources
Helixi64 – 663Combined sources
Beta strandi72 – 787Combined sources
Beta strandi81 – 877Combined sources
Beta strandi93 – 997Combined sources
Turni101 – 1033Combined sources
Beta strandi110 – 1145Combined sources
Turni121 – 1233Combined sources
Beta strandi133 – 1353Combined sources
Helixi139 – 1424Combined sources
Helixi155 – 1573Combined sources
Beta strandi162 – 1687Combined sources
Beta strandi171 – 1766Combined sources
Beta strandi178 – 1803Combined sources
Helixi183 – 1875Combined sources
Helixi188 – 1903Combined sources
Helixi191 – 1988Combined sources
Beta strandi199 – 2013Combined sources
Beta strandi205 – 2073Combined sources
Beta strandi212 – 2187Combined sources
Helixi220 – 22910Combined sources
Helixi232 – 2354Combined sources
Turni236 – 2394Combined sources
Helixi240 – 2467Combined sources
Turni253 – 2553Combined sources
Beta strandi262 – 2665Combined sources
Beta strandi268 – 2714Combined sources
Beta strandi273 – 2797Combined sources
Helixi282 – 29716Combined sources
Helixi300 – 3089Combined sources
Helixi310 – 3123Combined sources
Helixi316 – 3183Combined sources
Beta strandi319 – 3268Combined sources
Turni327 – 3293Combined sources
Beta strandi330 – 3323Combined sources
Turni334 – 3363Combined sources
Beta strandi338 – 3447Combined sources
Beta strandi350 – 35910Combined sources
Helixi364 – 37815Combined sources
Helixi385 – 39814Combined sources
Helixi403 – 4053Combined sources
Turni413 – 4175Combined sources
Beta strandi419 – 4213Combined sources
Beta strandi423 – 4253Combined sources
Beta strandi427 – 4337Combined sources
Helixi436 – 45015Combined sources
Helixi454 – 4574Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2XR8X-ray2.49A/C/E/G/I/K/M/O/Q/S/U/W1-459[»]
2XRXX-ray2.42A/C/E/G/I/K/M/O/Q/S/U/W1-459[»]
2XSHX-ray2.29A/C/E/G/I/K1-459[»]
2XSOX-ray2.20A/C/E/G/I/K/M/O/Q/S/U/W1-459[»]
2YFIX-ray2.15A/C/E/G/I/K1-459[»]
2YFJX-ray2.15A/C/E/G/I/K1-459[»]
2YFLX-ray2.60A/C/E/G/I/K1-459[»]
ProteinModelPortaliP37333.
SMRiP37333. Positions 18-458.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP37333.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini58 – 15699RieskePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 Rieske domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105FUY. Bacteria.
COG4638. LUCA.
HOGENOMiHOG000105925.
KOiK08689.
OMAiFREPKAQ.
OrthoDBiEOG6W19DT.

Family and domain databases

Gene3Di2.102.10.10. 1 hit.
3.90.380.10. 1 hit.
InterProiIPR017941. Rieske_2Fe-2S.
IPR015881. Ring-hydroxy_dOase_2Fe2S_BS.
IPR015879. Ring_hydroxy_dOase_asu_C_dom.
IPR001663. Rng_hydr_dOase-A.
[Graphical view]
PfamiPF00355. Rieske. 1 hit.
PF00848. Ring_hydroxyl_A. 1 hit.
[Graphical view]
PRINTSiPR00090. RNGDIOXGNASE.
SUPFAMiSSF50022. SSF50022. 1 hit.
PROSITEiPS51296. RIESKE. 1 hit.
PS00570. RING_HYDROXYL_ALPHA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P37333-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSAIKEVQG APVKWVTNWT PEAIRGLVDQ EKGLLDPRIY ADQSLYELEL
60 70 80 90 100
ERVFGRSWLL LGHESHVPET GDFLATYMGE DPVVMVRQKD KSIKVFLNQC
110 120 130 140 150
RHRGMRICRS DAGNAKAFTC SYHGWAYDIA GKLVNVPFEK EAFCDKKEGD
160 170 180 190 200
CGFDKAEWGP LQARVATYKG LVFANWDVQA PDLETYLGDA RPYMDVMLDR
210 220 230 240 250
TPAGTVAIGG MQKWVIPCNW KFAAEQFCSD MYHAGTTTHL SGILAGIPPE
260 270 280 290 300
MDLSQAQIPT KGNQFRAAWG GHGSGWYVDE PGSLLAVMGP KVTQYWTEGP
310 320 330 340 350
AAELAEQRLG HTGMPVRRMV GQHMTIFPTC SFLPTFNNIR IWHPRGPNEI
360 370 380 390 400
EVWAFTLVDA DAPAEIKEEY RRHNIRNFSA GGVFEQDDGE NWVEIQKGLR
410 420 430 440 450
GYKAKSQPLN AQMGLGRSQT GHPDFPGNVG YVYAEEAARG MYHHWMRMMS

EPSWATLKP
Length:459
Mass (Da):51,513
Last modified:January 23, 2007 - v3
Checksum:i54794B7146730A8F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M86348 Genomic DNA. Translation: AAB63425.1.
CP000272 Genomic DNA. Translation: ABE37059.1.
RefSeqiWP_011494299.1. NZ_CP008761.1.

Genome annotation databases

EnsemblBacteriaiABE37059; ABE37059; Bxe_C1197.
GeneIDi4010709.
KEGGibxb:DR64_8608.
bxe:Bxe_C1197.
PATRICi19343379. VBIBurXen52548_8947.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M86348 Genomic DNA. Translation: AAB63425.1.
CP000272 Genomic DNA. Translation: ABE37059.1.
RefSeqiWP_011494299.1. NZ_CP008761.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2XR8X-ray2.49A/C/E/G/I/K/M/O/Q/S/U/W1-459[»]
2XRXX-ray2.42A/C/E/G/I/K/M/O/Q/S/U/W1-459[»]
2XSHX-ray2.29A/C/E/G/I/K1-459[»]
2XSOX-ray2.20A/C/E/G/I/K/M/O/Q/S/U/W1-459[»]
2YFIX-ray2.15A/C/E/G/I/K1-459[»]
2YFJX-ray2.15A/C/E/G/I/K1-459[»]
2YFLX-ray2.60A/C/E/G/I/K1-459[»]
ProteinModelPortaliP37333.
SMRiP37333. Positions 18-458.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi266265.Bxe_C1197.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABE37059; ABE37059; Bxe_C1197.
GeneIDi4010709.
KEGGibxb:DR64_8608.
bxe:Bxe_C1197.
PATRICi19343379. VBIBurXen52548_8947.

Phylogenomic databases

eggNOGiENOG4105FUY. Bacteria.
COG4638. LUCA.
HOGENOMiHOG000105925.
KOiK08689.
OMAiFREPKAQ.
OrthoDBiEOG6W19DT.

Enzyme and pathway databases

UniPathwayiUPA00155; UER00250.
BioCyciBXEN266265:GJII-8849-MONOMER.
BRENDAi1.14.12.18. 7691.

Miscellaneous databases

EvolutionaryTraceiP37333.

Family and domain databases

Gene3Di2.102.10.10. 1 hit.
3.90.380.10. 1 hit.
InterProiIPR017941. Rieske_2Fe-2S.
IPR015881. Ring-hydroxy_dOase_2Fe2S_BS.
IPR015879. Ring_hydroxy_dOase_asu_C_dom.
IPR001663. Rng_hydr_dOase-A.
[Graphical view]
PfamiPF00355. Rieske. 1 hit.
PF00848. Ring_hydroxyl_A. 1 hit.
[Graphical view]
PRINTSiPR00090. RNGDIOXGNASE.
SUPFAMiSSF50022. SSF50022. 1 hit.
PROSITEiPS51296. RIESKE. 1 hit.
PS00570. RING_HYDROXYL_ALPHA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400."
    Erickson B.D., Mondello F.J.
    J. Bacteriol. 174:2903-2912(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LB400.
  3. "Purification and characterization of the oxygenase component of biphenyl 2,3-dioxygenase from Pseudomonas sp. strain LB400."
    Haddock J.D., Gibson D.T.
    J. Bacteriol. 177:5834-5839(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-11, CHARACTERIZATION.
  4. Erratum
    Haddock J.D., Gibson D.T.
    J. Bacteriol. 178:2158-2158(1996)

Entry informationi

Entry nameiBPHA_BURXL
AccessioniPrimary (citable) accession number: P37333
Secondary accession number(s): Q13FT0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: January 23, 2007
Last modified: November 11, 2015
This is version 107 of the entry and version 3 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.