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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)DescriptionActionsGraphical viewLength
Metal bindingi98Iron-sulfur (2Fe-2S)1 PublicationImported1
Metal bindingi100Iron-sulfur (2Fe-2S); via pros nitrogen1 PublicationImported1
Metal bindingi118Iron-sulfur (2Fe-2S)1 PublicationImported1
Metal bindingi121Iron-sulfur (2Fe-2S); via pros nitrogen1 PublicationImported1
Metal bindingi224Iron; via tele nitrogen1 PublicationImported1
Metal bindingi230Iron; via tele nitrogen1 PublicationImported1
Metal bindingi378Iron1 PublicationImported1

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

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)DescriptionActionsGraphical viewLength
ChainiPRO_00004306591 – 460Biphenyl 2,3-dioxygenase subunit alphaAdd BLAST460

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 interactor.

Structurei

Secondary structure

1460
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi19 – 23Combined sources5
Turni28 – 31Combined sources4
Helixi35 – 38Combined sources4
Helixi41 – 50Combined sources10
Turni51 – 54Combined sources4
Beta strandi57 – 61Combined sources5
Helixi62 – 64Combined sources3
Beta strandi70 – 76Combined sources7
Beta strandi79 – 85Combined sources7
Beta strandi91 – 96Combined sources6
Turni99 – 101Combined sources3
Beta strandi108 – 112Combined sources5
Turni119 – 121Combined sources3
Beta strandi131 – 133Combined sources3
Helixi137 – 140Combined sources4
Helixi146 – 148Combined sources3
Beta strandi153 – 159Combined sources7
Beta strandi162 – 166Combined sources5
Helixi174 – 178Combined sources5
Helixi181 – 189Combined sources9
Beta strandi196 – 198Combined sources3
Beta strandi203 – 207Combined sources5
Helixi211 – 220Combined sources10
Helixi222 – 226Combined sources5
Turni227 – 230Combined sources4
Helixi231 – 236Combined sources6
Beta strandi253 – 257Combined sources5
Beta strandi259 – 262Combined sources4
Beta strandi264 – 270Combined sources7
Helixi273 – 288Combined sources16
Helixi291 – 299Combined sources9
Helixi303 – 307Combined sources5
Beta strandi308 – 316Combined sources9
Turni317 – 319Combined sources3
Beta strandi320 – 322Combined sources3
Turni324 – 326Combined sources3
Beta strandi328 – 334Combined sources7
Beta strandi340 – 349Combined sources10
Helixi354 – 367Combined sources14
Helixi375 – 388Combined sources14
Helixi393 – 395Combined sources3
Turni403 – 406Combined sources4
Beta strandi408 – 410Combined sources3
Beta strandi413 – 415Combined sources3
Beta strandi417 – 423Combined sources7
Helixi426 – 439Combined sources14
Helixi444 – 448Combined sources5

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ53122.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini56 – 165RieskePROSITE-ProRule annotationAdd BLAST110

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni217 – 230Substrate binding1 PublicationAdd BLAST14

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ULIX-ray2.20A/C/E1-460[»]
1ULJX-ray2.60A/C/E1-460[»]
ProteinModelPortaliQ53122.
SMRiQ53122.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ53122. 1 interactor.

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.

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: November 2, 2016
This is version 108 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.