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Protein

Biphenyl 2,3-dioxygenase subunit alpha

Gene

bphA1

Organism
Rhodococcus jostii (strain RHA1)
Status
Reviewed-Annotation score: Annotation score: 5 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 essential for biphenyl degradation and 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 BphA3.2 Publications

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • [2Fe-2S] cluster1 PublicationNote: Binds 1 [2Fe-2S] cluster per subunit.1 Publication
  • Fe cation1 PublicationNote: Binds 1 Fe cation per subunit.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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi98 – 981Iron-sulfur (2Fe-2S)1 PublicationImported
Metal bindingi100 – 1001Iron-sulfur (2Fe-2S); via pros nitrogen1 PublicationImported
Metal bindingi118 – 1181Iron-sulfur (2Fe-2S)1 PublicationImported
Metal bindingi121 – 1211Iron-sulfur (2Fe-2S); via pros nitrogen1 PublicationImported
Metal bindingi224 – 2241Iron; via tele nitrogen1 PublicationImported
Metal bindingi230 – 2301Iron; via tele nitrogen1 PublicationImported
Metal bindingi378 – 3781Iron1 PublicationImported

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

BioCyciRJOS101510:GJJ1-7339-MONOMER.
UniPathwayiUPA00155; UER00250.

Names & Taxonomyi

Protein namesi
Recommended name:
Biphenyl 2,3-dioxygenase subunit alphaCurated (EC:1.14.12.181 Publication)
Alternative name(s):
Biphenyl dioxygenase system, oxygenase component subunit alphaCurated
Short name:
BDO, oxygenase component subunit alphaCurated
Rieske dioxygenase1 Publication
Terminal oxygenase component of biphenyl dioxygenase, large subunit1 Publication
Gene namesi
Name:bphA11 Publication
Synonyms:bphAaImported
Ordered Locus Names:RHA1_ro08060Imported
Encoded oniPlasmid pRHL1Imported
OrganismiRhodococcus jostii (strain RHA1)
Taxonomic identifieri101510 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus
Proteomesi
  • UP000008710 Componenti: Plasmid pRHL1

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene lose their ability to grow on biphenyl.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 460460Biphenyl 2,3-dioxygenase subunit alphaPRO_0000430659Add
BLAST

Proteomic databases

PRIDEiQ53122.

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
bphA2Q531232EBI-1040100,EBI-1040088

Protein-protein interaction databases

IntActiQ53122. 1 interaction.

Structurei

Secondary structure

1
460
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi19 – 235Combined sources
Turni28 – 314Combined sources
Helixi35 – 384Combined sources
Helixi41 – 5010Combined sources
Turni51 – 544Combined sources
Beta strandi57 – 615Combined sources
Helixi62 – 643Combined sources
Beta strandi70 – 767Combined sources
Beta strandi79 – 857Combined sources
Beta strandi91 – 966Combined sources
Turni99 – 1013Combined sources
Beta strandi108 – 1125Combined sources
Turni119 – 1213Combined sources
Beta strandi131 – 1333Combined sources
Helixi137 – 1404Combined sources
Helixi146 – 1483Combined sources
Beta strandi153 – 1597Combined sources
Beta strandi162 – 1665Combined sources
Helixi174 – 1785Combined sources
Helixi181 – 1899Combined sources
Beta strandi196 – 1983Combined sources
Beta strandi203 – 2075Combined sources
Helixi211 – 22010Combined sources
Helixi222 – 2265Combined sources
Turni227 – 2304Combined sources
Helixi231 – 2366Combined sources
Beta strandi253 – 2575Combined sources
Beta strandi259 – 2624Combined sources
Beta strandi264 – 2707Combined sources
Helixi273 – 28816Combined sources
Helixi291 – 2999Combined sources
Helixi303 – 3075Combined sources
Beta strandi308 – 3169Combined sources
Turni317 – 3193Combined sources
Beta strandi320 – 3223Combined sources
Turni324 – 3263Combined sources
Beta strandi328 – 3347Combined sources
Beta strandi340 – 34910Combined sources
Helixi354 – 36714Combined sources
Helixi375 – 38814Combined sources
Helixi393 – 3953Combined sources
Turni403 – 4064Combined sources
Beta strandi408 – 4103Combined sources
Beta strandi413 – 4153Combined sources
Beta strandi417 – 4237Combined sources
Helixi426 – 43914Combined sources
Helixi444 – 4485Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ULIX-ray2.20A/C/E1-460[»]
1ULJX-ray2.60A/C/E1-460[»]
ProteinModelPortaliQ53122.
SMRiQ53122. Positions 17-451.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ53122.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini56 – 165110RieskePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni217 – 23014Substrate binding1 PublicationAdd
BLAST

Sequence similaritiesi

Contains 1 Rieske domain.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000105925.
KOiK08689.
OMAiSITHNTI.
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.

Q53122-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDVQCEPAL AGRKPKWADA DIAELVDERT GRLDPRIYTD EALYEQELER
60 70 80 90 100
IFGRSWLLMG HETQIPKAGD FMTNYMGEDP VMVVRQKNGE IRVFLNQCRH
110 120 130 140 150
RGMRICRADG GNAKSFTCSY HGWAYDTGGN LVSVPFEEQA FPGLRKEDWG
160 170 180 190 200
PLQARVETYK GLIFANWDAD APDLDTYLGE AKFYMDHMLD RTEAGTEAIP
210 220 230 240 250
GIQKWVIPCN WKFAAEQFCS DMYHAGTTSH LSGILAGLPD GVDLSELAPP
260 270 280 290 300
TEGIQYRATW GGHGSGFYIG DPNLLLAIMG PKVTEYWTQG PAAEKASERL
310 320 330 340 350
GSTERGQQLM AQHMTIFPTC SFLPGINTIR AWHPRGPNEI EVWAFTVVDA
360 370 380 390 400
DAPEEMKEEY RQQTLRTFSA GGVFEQDDGE NWVEIQQVLR GHKARSRPFN
410 420 430 440 450
AEMGLGQTDS DNPDYPGTIS YVYSEEAARG LYTQWVRMMT SPDWAALDAT
460
RPAVSESTHT
Length:460
Mass (Da):51,592
Last modified:November 1, 1996 - v1
Checksum:i28D86F926FA4E9A0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000432 Genomic DNA. Translation: ABG99107.1.
D32142 Genomic DNA. Translation: BAA06868.1.
RefSeqiWP_011599002.1. NC_008269.1.

Genome annotation databases

EnsemblBacteriaiABG99107; ABG99107; RHA1_ro08060.
GeneIDi4225185.
KEGGirha:RHA1_ro08060.
PATRICi23213686. VBIRhoJos26306_7407.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000432 Genomic DNA. Translation: ABG99107.1.
D32142 Genomic DNA. Translation: BAA06868.1.
RefSeqiWP_011599002.1. NC_008269.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ULIX-ray2.20A/C/E1-460[»]
1ULJX-ray2.60A/C/E1-460[»]
ProteinModelPortaliQ53122.
SMRiQ53122. Positions 17-451.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ53122. 1 interaction.

Proteomic databases

PRIDEiQ53122.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABG99107; ABG99107; RHA1_ro08060.
GeneIDi4225185.
KEGGirha:RHA1_ro08060.
PATRICi23213686. VBIRhoJos26306_7407.

Phylogenomic databases

HOGENOMiHOG000105925.
KOiK08689.
OMAiSITHNTI.
OrthoDBiPOG091H0936.

Enzyme and pathway databases

UniPathwayiUPA00155; UER00250.
BioCyciRJOS101510:GJJ1-7339-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ53122.

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 nameiBPHA1_RHOJR
AccessioniPrimary (citable) accession number: Q53122
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 29, 2014
Last sequence update: November 1, 1996
Last modified: September 7, 2016
This is version 106 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.