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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)DescriptionActionsGraphical viewLength
Metal bindingi100Iron-sulfur (2Fe-2S)PROSITE-ProRule annotation1
Metal bindingi102Iron-sulfur (2Fe-2S); via pros nitrogenPROSITE-ProRule annotation1
Metal bindingi120Iron-sulfur (2Fe-2S)PROSITE-ProRule annotation1
Metal bindingi123Iron-sulfur (2Fe-2S); via pros nitrogenPROSITE-ProRule annotation1
Metal bindingi233IronBy similarity1
Metal bindingi239IronBy similarity1

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

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 lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
Proteomesi
  • UP000001817 Componenti: Chromosome 3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000850462 – 459Biphenyl dioxygenase subunit alphaAdd BLAST458

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

1459
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi21 – 25Combined sources5
Turni30 – 33Combined sources4
Helixi37 – 40Combined sources4
Helixi43 – 52Combined sources10
Turni53 – 56Combined sources4
Beta strandi59 – 63Combined sources5
Helixi64 – 66Combined sources3
Beta strandi72 – 78Combined sources7
Beta strandi81 – 87Combined sources7
Beta strandi93 – 98Combined sources6
Turni101 – 103Combined sources3
Beta strandi110 – 114Combined sources5
Turni121 – 123Combined sources3
Beta strandi133 – 135Combined sources3
Helixi139 – 142Combined sources4
Helixi155 – 157Combined sources3
Beta strandi164 – 168Combined sources5
Beta strandi171 – 176Combined sources6
Beta strandi178 – 180Combined sources3
Helixi183 – 187Combined sources5
Helixi188 – 190Combined sources3
Helixi191 – 198Combined sources8
Beta strandi199 – 201Combined sources3
Beta strandi205 – 207Combined sources3
Beta strandi212 – 218Combined sources7
Helixi220 – 229Combined sources10
Turni232 – 239Combined sources8
Helixi240 – 245Combined sources6
Helixi253 – 255Combined sources3
Beta strandi262 – 266Combined sources5
Beta strandi268 – 271Combined sources4
Beta strandi273 – 279Combined sources7
Helixi281 – 297Combined sources17
Helixi300 – 308Combined sources9
Turni309 – 313Combined sources5
Helixi316 – 318Combined sources3
Beta strandi319 – 326Combined sources8
Turni327 – 329Combined sources3
Beta strandi330 – 332Combined sources3
Turni334 – 336Combined sources3
Beta strandi338 – 344Combined sources7
Beta strandi350 – 359Combined sources10
Helixi364 – 377Combined sources14
Helixi385 – 398Combined sources14
Helixi403 – 405Combined sources3
Turni413 – 416Combined sources4
Beta strandi419 – 421Combined sources3
Beta strandi423 – 425Combined sources3
Beta strandi427 – 433Combined sources7
Helixi436 – 450Combined sources15
Helixi454 – 457Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5AEUX-ray2.49A/C/E/G1-459[»]
5AEWX-ray1.88A/C/E/G/I/K/M/O/Q/S/U/W1-459[»]
ProteinModelPortaliP37333.
SMRiP37333.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP37333.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini58 – 156RieskePROSITE-ProRule annotationAdd BLAST99

Sequence similaritiesi

Contains 1 Rieske domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105FUY. Bacteria.
COG4638. LUCA.
HOGENOMiHOG000105925.
KOiK08689.
OMAiFREPKAQ.
OrthoDBiPOG091H0936.

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
PDB 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[»]
5AEUX-ray2.49A/C/E/G1-459[»]
5AEWX-ray1.88A/C/E/G/I/K/M/O/Q/S/U/W1-459[»]
ProteinModelPortaliP37333.
SMRiP37333.
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.
OrthoDBiPOG091H0936.

Enzyme and pathway databases

UniPathwayiUPA00155; UER00250.
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...

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 2, 2016
This is version 112 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.