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Protein

Biphenyl 2,3-dioxygenase subunit beta

Gene

bphA2

Organism
Rhodococcus jostii (strain RHA1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Part of the oxygenase component of the biphenyl dioxygenase system that catalyzes the stereospecific dihydroxylation of the aromatic ring of biphenyl, yielding a dihydrodiol compound. Is likely involved in biphenyl degradation that allows growth of Rhodococcus sp. strain RHA1 on biphenyl as the sole source of carbon and energy. Can also use naphtalene and 4-chlorobiphenyl (4-CB) as substrates, as well as some polychlorinated biphenyls (PCB) such as 2,2'-dichlorobiphenyl, 2,3-dichlorobiphenyl and 2,5,2'-trichlorobiphenyl. Exhibits weak activity toward dibenzofuran and dibenzo-p-dioxin. Electrons are transferred from NADH to the [2Fe-2S] cluster in BphA1 via FAD of BphA4 and [2Fe-2S] cluster of BphA3.1 Publication1 Publication

Catalytic activityi

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

Pathwayi: biphenyl degradation

This protein is involved in step 1 of the subpathway that synthesizes 2-hydroxy-2,4-pentadienoate and benzoate from biphenyl.1 Publication
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Biphenyl 2,3-dioxygenase subunit beta (bphA2), Biphenyl 2,3-dioxygenase subunit alpha (bphA1)
  2. no protein annotated in this organism
  3. no protein annotated in this organism
  4. no protein annotated in this organism
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.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

Aromatic hydrocarbons catabolism

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciRJOS101510:GJJ1-7338-MONOMER.
UniPathwayiUPA00155; UER00250.

Names & Taxonomyi

Protein namesi
Recommended name:
Biphenyl 2,3-dioxygenase subunit betaCurated (EC:1.14.12.181 Publication)
Alternative name(s):
Biphenyl dioxygenase system, oxygenase component subunit betaCurated
Short name:
BDO, oxygenase component subunit betaCurated
Terminal oxygenase component of biphenyl dioxygenase, small subunit1 Publication
Gene namesi
Name:bphA21 Publication
Synonyms:bphAbImported
Ordered Locus Names:RHA1_ro08059Imported
Encoded oniPlasmid pRHL1Imported
OrganismiRhodococcus jostii (strain RHA1)
Taxonomic identifieri101510 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus
Proteomesi
  • UP000008710 Componenti: Plasmid pRHL1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 187187Biphenyl 2,3-dioxygenase subunit betaPRO_0000430660Add
BLAST

Proteomic databases

PRIDEiQ53123.

Expressioni

Inductioni

Transcription is up-regulated by aromatic compounds including biphenyl, ethylbenzene, benzene, toluene, xylene, cumene, cymene, and chlorinated benzenes. Is under the control of the BphST two-component regulatory system.1 Publication

Interactioni

Subunit structurei

Heterohexamer consisting of three BphA1 subunits and three BphA2 subunits. The multicomponent biphenyl dioxygenase system is composed of a ferredoxin reductase (BphA4), a ferredoxin (BphA3), and a terminal oxygenase (BphA1A2).1 Publication1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
bphA1Q531222EBI-1040088,EBI-1040100

Protein-protein interaction databases

IntActiQ53123. 1 interaction.

Structurei

Secondary structure

1
187
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi20 – 3819Combined sources
Helixi42 – 476Combined sources
Beta strandi49 – 5810Combined sources
Helixi65 – 706Combined sources
Beta strandi79 – 835Combined sources
Helixi85 – 9511Combined sources
Helixi101 – 1033Combined sources
Beta strandi108 – 12013Combined sources
Beta strandi126 – 13914Combined sources
Turni140 – 1423Combined sources
Beta strandi143 – 15715Combined sources
Beta strandi159 – 1624Combined sources
Beta strandi164 – 17411Combined sources
Beta strandi176 – 1816Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ULIX-ray2.20B/D/F1-187[»]
1ULJX-ray2.60B/D/F1-187[»]
ProteinModelPortaliQ53123.
SMRiQ53123. Positions 10-187.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ53123.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000106036.
KOiK15750.
OrthoDBiEOG6M9DWF.

Family and domain databases

Gene3Di3.10.450.50. 1 hit.
InterProiIPR032710. NTF2-like_dom.
IPR000391. Rng_hydr_dOase-bsu.
[Graphical view]
PfamiPF00866. Ring_hydroxyl_B. 1 hit.
[Graphical view]
SUPFAMiSSF54427. SSF54427. 1 hit.

Sequencei

Sequence statusi: Complete.

Q53123-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIDAESPTTA FRTKPAPVDP SLQHEIEQFY YWEAKLLNDR RFQEWFDLLA
60 70 80 90 100
EDIHYFMPIR TTRIMRETAQ EYSGAREYAH FDDNAQMMRG RLRKITSDVS
110 120 130 140 150
WSENPASRTR HVISNVMIVD GEKPGEYHVS SVFIVYRNRL ERQLDIFAGE
160 170 180
RKDILRRTGS EAGFELAKRT ILIDQSTILS NNLSFFF
Length:187
Mass (Da):22,020
Last modified:November 1, 1996 - v1
Checksum:i896AE86BC80F215C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D32142 Genomic DNA. Translation: BAA06869.1.
CP000432 Genomic DNA. Translation: ABG99106.1.
RefSeqiWP_011599001.1. NC_008269.1.

Genome annotation databases

EnsemblBacteriaiABG99106; ABG99106; RHA1_ro08059.
GeneIDi4225184.
KEGGirha:RHA1_ro08059.
PATRICi23213684. VBIRhoJos26306_7406.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D32142 Genomic DNA. Translation: BAA06869.1.
CP000432 Genomic DNA. Translation: ABG99106.1.
RefSeqiWP_011599001.1. NC_008269.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ULIX-ray2.20B/D/F1-187[»]
1ULJX-ray2.60B/D/F1-187[»]
ProteinModelPortaliQ53123.
SMRiQ53123. Positions 10-187.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ53123. 1 interaction.

Proteomic databases

PRIDEiQ53123.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABG99106; ABG99106; RHA1_ro08059.
GeneIDi4225184.
KEGGirha:RHA1_ro08059.
PATRICi23213684. VBIRhoJos26306_7406.

Phylogenomic databases

HOGENOMiHOG000106036.
KOiK15750.
OrthoDBiEOG6M9DWF.

Enzyme and pathway databases

UniPathwayiUPA00155; UER00250.
BioCyciRJOS101510:GJJ1-7338-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ53123.

Family and domain databases

Gene3Di3.10.450.50. 1 hit.
InterProiIPR032710. NTF2-like_dom.
IPR000391. Rng_hydr_dOase-bsu.
[Graphical view]
PfamiPF00866. Ring_hydroxyl_B. 1 hit.
[Graphical view]
SUPFAMiSSF54427. SSF54427. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of biphenyl catabolic genes of gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1."
    Masai E., Yamada A., Healy J.M., Hatta T., Kimbara K., Fukuda M., Yano K.
    Appl. Environ. Microbiol. 61:2079-2085(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PATHWAY.
    Strain: RHA1.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RHA1.
  3. "Characterization of transcriptional regulatory genes for biphenyl degradation in Rhodococcus sp. strain RHA1."
    Takeda H., Yamada A., Miyauchi K., Masai E., Fukuda M.
    J. Bacteriol. 186:2134-2146(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: RHA1.
  4. "Characterization of two biphenyl dioxygenases for biphenyl/PCB degradation in A PCB degrader, Rhodococcus sp. strain RHA1."
    Iwasaki T., Takeda H., Miyauchi K., Yamada T., Masai E., Fukuda M.
    Biosci. Biotechnol. Biochem. 71:993-1002(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
    Strain: RHA1.
  5. "Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1."
    Furusawa Y., Nagarajan V., Tanokura M., Masai E., Fukuda M., Senda T.
    J. Mol. Biol. 342:1041-1052(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH ALPHA SUBUNIT.
    Strain: RHA1.

Entry informationi

Entry nameiBPHA2_RHOJR
AccessioniPrimary (citable) accession number: Q53123
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 29, 2014
Last sequence update: November 1, 1996
Last modified: January 20, 2016
This is version 96 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, Complete proteome, Plasmid, 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.