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Protein

Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase

Gene

bphB

Organism
Burkholderia xenovorans (strain LB400)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH.

Pathwayi: biphenyl degradation

This protein is involved in step 2 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 alpha (bphA), Biphenyl dioxygenase subunit beta (bphE)
  2. Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (bphB)
  3. Biphenyl-2,3-diol 1,2-dioxygenase (bphC)
  4. 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
Binding sitei59NAD1 Publication1
Binding sitei142SubstrateBy similarity1
Active sitei155Proton acceptor1
Binding sitei159NAD1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi9 – 36NAD1 PublicationAdd BLAST28

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Aromatic hydrocarbons catabolism

Keywords - Ligandi

NAD

Enzyme and pathway databases

BRENDAi1.3.1.56. 5085.
UniPathwayiUPA00155; UER00251.

Names & Taxonomyi

Protein namesi
Recommended name:
Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC:1.3.1.56)
Alternative name(s):
2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase
2,3-dihydroxy-4-phenylhexa-4,6-diene dehydrogenase
Biphenyl-2,3-dihydro-2,3-diol dehydrogenase
Biphenyl-cis-diol dehydrogenase
Gene namesi
Name:bphB
Ordered Locus Names:Bxeno_C1126
ORF Names:Bxe_C1192
OrganismiBurkholderia xenovorans (strain LB400)
Taxonomic identifieri266265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
Proteomesi
  • UP000001817 Componenti: Chromosome 3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000545311 – 277Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenaseAdd BLAST277

Interactioni

Protein-protein interaction databases

STRINGi266265.Bxe_C1192.

Structurei

Secondary structure

1277
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni2 – 5Combined sources4
Beta strandi7 – 11Combined sources5
Turni12 – 14Combined sources3
Helixi16 – 27Combined sources12
Beta strandi31 – 37Combined sources7
Helixi39 – 49Combined sources11
Helixi50 – 52Combined sources3
Beta strandi53 – 57Combined sources5
Helixi63 – 77Combined sources15
Beta strandi82 – 84Combined sources3
Helixi96 – 98Combined sources3
Turni101 – 103Combined sources3
Helixi104 – 115Combined sources12
Helixi117 – 133Combined sources17
Beta strandi136 – 140Combined sources5
Helixi143 – 145Combined sources3
Helixi153 – 173Combined sources21
Turni174 – 176Combined sources3
Beta strandi178 – 184Combined sources7
Helixi195 – 197Combined sources3
Helixi209 – 213Combined sources5
Turni214 – 216Combined sources3
Helixi225 – 228Combined sources4
Helixi230 – 236Combined sources7
Helixi238 – 241Combined sources4
Beta strandi248 – 254Combined sources7
Helixi255 – 257Combined sources3
Helixi269 – 273Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BDBX-ray2.00A1-277[»]
ProteinModelPortaliP47227.
SMRiP47227.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP47227.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108QJ2. Bacteria.
ENOG410XQCB. LUCA.
KOiK08690.
OMAiEVFHINV.
OrthoDBiPOG091H0C0P.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR017711. BphB_TodD.
IPR016040. NAD(P)-bd_dom.
IPR020904. Sc_DH/Rdtase_CS.
IPR002347. SDR_fam.
[Graphical view]
PANTHERiPTHR24322. PTHR24322. 2 hits.
PfamiPF00106. adh_short. 1 hit.
[Graphical view]
PRINTSiPR00081. GDHRDH.
PR00080. SDRFAMILY.
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR03325. BphB_TodD. 1 hit.
PROSITEiPS00061. ADH_SHORT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P47227-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLKGEAVLI TGGASGLGRA LVDRFVAEGA KVAVLDKSAE RLAELETDHG
60 70 80 90 100
DNVLGIVGDV RSLEDQKQAA SRCVARFGKI DTLIPNAGIW DYSTALVDLP
110 120 130 140 150
EESLDAAFDE VFHINVKGYI HAVKACLPAL VASRGNVIFT ISNAGFYPNG
160 170 180 190 200
GGPLYTAAKH AIVGLVRELA FELAPYVRVN GVGSGGINSD LRGPSSLGMG
210 220 230 240 250
SKAISTVPLA DMLKSVLPIG RMPEVEEYTG AYVFFATRGD AAPATGALLN
260 270
YDGGLGVRGF FSGAGGNDLL EQLNIHP
Length:277
Mass (Da):28,901
Last modified:February 1, 1996 - v1
Checksum:i00194120BD4E12D1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X66122 Genomic DNA. Translation: CAA46909.1.
CP000272 Genomic DNA. Translation: ABE37054.1.
M86348 Genomic DNA. Translation: AAB63430.2.
PIRiJN0814.
RefSeqiWP_011494296.1. NZ_CP008761.1.

Genome annotation databases

EnsemblBacteriaiABE37054; ABE37054; Bxe_C1192.
GeneIDi4010704.
KEGGibxb:DR64_8613.
bxe:Bxe_C1192.
PATRICi19343369. VBIBurXen52548_8942.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X66122 Genomic DNA. Translation: CAA46909.1.
CP000272 Genomic DNA. Translation: ABE37054.1.
M86348 Genomic DNA. Translation: AAB63430.2.
PIRiJN0814.
RefSeqiWP_011494296.1. NZ_CP008761.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BDBX-ray2.00A1-277[»]
ProteinModelPortaliP47227.
SMRiP47227.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi266265.Bxe_C1192.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABE37054; ABE37054; Bxe_C1192.
GeneIDi4010704.
KEGGibxb:DR64_8613.
bxe:Bxe_C1192.
PATRICi19343369. VBIBurXen52548_8942.

Phylogenomic databases

eggNOGiENOG4108QJ2. Bacteria.
ENOG410XQCB. LUCA.
KOiK08690.
OMAiEVFHINV.
OrthoDBiPOG091H0C0P.

Enzyme and pathway databases

UniPathwayiUPA00155; UER00251.
BRENDAi1.3.1.56. 5085.

Miscellaneous databases

EvolutionaryTraceiP47227.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR017711. BphB_TodD.
IPR016040. NAD(P)-bd_dom.
IPR020904. Sc_DH/Rdtase_CS.
IPR002347. SDR_fam.
[Graphical view]
PANTHERiPTHR24322. PTHR24322. 2 hits.
PfamiPF00106. adh_short. 1 hit.
[Graphical view]
PRINTSiPR00081. GDHRDH.
PR00080. SDRFAMILY.
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR03325. BphB_TodD. 1 hit.
PROSITEiPS00061. ADH_SHORT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiBPHB_BURXL
AccessioniPrimary (citable) accession number: P47227
Secondary accession number(s): Q13FT5, Q52435
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: November 2, 2016
This is version 125 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, 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.