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Protein

Biphenyl dioxygenase subunit alpha

Gene

bphA

Organism
Comamonas testosteroni (Pseudomonas testosteroni)
Status
Reviewed-Annotation score: Annotation score: 3 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:
  • [2Fe-2S] clusterPROSITE-ProRule annotationNote: Binds 1 [2Fe-2S] cluster per subunit.PROSITE-ProRule annotation
  • Fe cationBy similarityNote: Binds 1 Fe cation per subunit.By similarity

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 beta (bphE), Biphenyl dioxygenase subunit alpha (bphA)
  2. Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (bphB)
  3. no protein annotated in this organism
  4. 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (bphD), 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. 1590.
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
OrganismiComamonas testosteroni (Pseudomonas testosteroni)
Taxonomic identifieri285 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeComamonas

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000850471 – 457Biphenyl dioxygenase subunit alphaAdd BLAST457

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 (By similarity).By similarity

Structurei

Secondary structure

1457
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi21 – 25Combined sources5
Turni30 – 33Combined sources4
Beta strandi34 – 36Combined sources3
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
Beta strandi116 – 119Combined sources4
Turni121 – 123Combined sources3
Beta strandi126 – 128Combined sources3
Beta strandi133 – 135Combined sources3
Helixi139 – 142Combined sources4
Beta strandi145 – 147Combined sources3
Turni148 – 151Combined sources4
Helixi155 – 157Combined sources3
Beta strandi162 – 168Combined sources7
Beta strandi171 – 176Combined sources6
Helixi183 – 186Combined sources4
Turni187 – 189Combined 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
Turni253 – 255Combined sources3
Beta strandi262 – 266Combined sources5
Beta strandi268 – 271Combined sources4
Beta strandi273 – 279Combined sources7
Helixi282 – 297Combined sources16
Helixi300 – 308Combined sources9
Helixi314 – 316Combined sources3
Beta strandi317 – 324Combined sources8
Turni325 – 327Combined sources3
Beta strandi328 – 330Combined sources3
Turni332 – 334Combined sources3
Beta strandi336 – 342Combined sources7
Beta strandi348 – 357Combined sources10
Helixi362 – 375Combined sources14
Helixi383 – 396Combined sources14
Helixi402 – 404Combined sources3
Beta strandi406 – 408Combined sources3
Turni411 – 414Combined sources4
Beta strandi423 – 431Combined sources9
Helixi434 – 448Combined sources15
Helixi452 – 455Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3GZXX-ray1.58A1-457[»]
3GZYX-ray1.62A1-457[»]
ProteinModelPortaliQ46372.
SMRiQ46372.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46372.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini58 – 174RieskePROSITE-ProRule annotationAdd BLAST117

Sequence similaritiesi

Contains 1 Rieske domain.PROSITE-ProRule annotation

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.

Q46372-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSTMKDTQE APVRWSRNWT PDAIRALVDQ DNGKLDARIY ADQDLYQLEL
60 70 80 90 100
ERVFGRSWLM LGHETHIPKI GDYLTTYMGE DPVIMVRQKD QSIKVFLNQC
110 120 130 140 150
RHRGMRIVRS DGGNAKAFTC TYHGWAYDIA GNLVNVPFEK EAFCDKKEGD
160 170 180 190 200
CGFDKADWGP LQARVETYKG LVFANWDPEA PDLKTYLSDA MPYMDVMLDR
210 220 230 240 250
TEAGTEAIGG IQKWVIPCNW KFAAEQFCSD MYHAGTMSHL SGVLAGLPPE
260 270 280 290 300
MDLTQIQLSK NGNQFRSAWG GHGAGWFIND SSILLSVVGP KITQYWTQGP
310 320 330 340 350
AAEKAARRVP QLPILDMFGQ HMTVFPTCSF LPGINTIRTW HPRGPNEVEV
360 370 380 390 400
WAFVLVDADA PEDIKEEFRL QNIRTFNAGG VFEQDDGENW VEIQRVMRGH
410 420 430 440 450
KAKSTSLCAK MGLNVPNKNN PAYPGKTAYV YAEEAARGMY HHWSRMMSEP

SWDTLKP
Length:457
Mass (Da):51,692
Last modified:November 1, 1996 - v1
Checksum:iD133FC0635FACBF5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U47637 Genomic DNA. Translation: AAC44526.1.
PIRiJC4993.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U47637 Genomic DNA. Translation: AAC44526.1.
PIRiJC4993.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3GZXX-ray1.58A1-457[»]
3GZYX-ray1.62A1-457[»]
ProteinModelPortaliQ46372.
SMRiQ46372.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00155; UER00250.
BRENDAi1.14.12.18. 1590.

Miscellaneous databases

EvolutionaryTraceiQ46372.

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_COMTE
AccessioniPrimary (citable) accession number: Q46372
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 79 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

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.