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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)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

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 457457Biphenyl dioxygenase subunit alphaPRO_0000085047Add
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 (By similarity).By similarity

Structurei

Secondary structure

1
457
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 255Combined sources
Turni30 – 334Combined sources
Beta strandi34 – 363Combined 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 – 986Combined sources
Turni101 – 1033Combined sources
Beta strandi110 – 1145Combined sources
Beta strandi116 – 1194Combined sources
Turni121 – 1233Combined sources
Beta strandi126 – 1283Combined sources
Beta strandi133 – 1353Combined sources
Helixi139 – 1424Combined sources
Beta strandi145 – 1473Combined sources
Turni148 – 1514Combined sources
Helixi155 – 1573Combined sources
Beta strandi162 – 1687Combined sources
Beta strandi171 – 1766Combined sources
Helixi183 – 1864Combined sources
Turni187 – 1893Combined sources
Helixi191 – 1988Combined sources
Beta strandi199 – 2013Combined sources
Beta strandi205 – 2073Combined sources
Beta strandi212 – 2187Combined sources
Helixi220 – 22910Combined sources
Turni232 – 2398Combined sources
Helixi240 – 2456Combined sources
Turni253 – 2553Combined sources
Beta strandi262 – 2665Combined sources
Beta strandi268 – 2714Combined sources
Beta strandi273 – 2797Combined sources
Helixi282 – 29716Combined sources
Helixi300 – 3089Combined sources
Helixi314 – 3163Combined sources
Beta strandi317 – 3248Combined sources
Turni325 – 3273Combined sources
Beta strandi328 – 3303Combined sources
Turni332 – 3343Combined sources
Beta strandi336 – 3427Combined sources
Beta strandi348 – 35710Combined sources
Helixi362 – 37514Combined sources
Helixi383 – 39614Combined sources
Helixi402 – 4043Combined sources
Beta strandi406 – 4083Combined sources
Turni411 – 4144Combined sources
Beta strandi423 – 4319Combined sources
Helixi434 – 44815Combined sources
Helixi452 – 4554Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3GZXX-ray1.58A1-457[»]
3GZYX-ray1.62A1-457[»]
ProteinModelPortaliQ46372.
SMRiQ46372. Positions 18-456.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46372.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini58 – 174117RieskePROSITE-ProRule annotationAdd
BLAST

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
EntryMethodResolution (Å)ChainPositionsPDBsum
3GZXX-ray1.58A1-457[»]
3GZYX-ray1.62A1-457[»]
ProteinModelPortaliQ46372.
SMRiQ46372. Positions 18-456.
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...

Publicationsi

  1. "Sequencing of Comamonas testosteroni strain B-356-biphenyl/chlorobiphenyl dioxygenase genes: evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases."
    Sylvestre M., Sirois M., Hurtubise Y., Bergeron J., Ahmad D., Shareck F., Barriault D., Guillemette I., Juteau J.-M.
    Gene 174:195-202(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: B-356.

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: October 14, 2015
This is version 77 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.