P47227 (BPHB_BURXL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	bphB
Ordered Locus Names:	Bxeno_C1126
ORF Names:	Bxe_C1192

Organism

Burkholderia xenovorans (strain LB400) [Complete proteome] [HAMAP]

Taxonomic identifier

266265 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Burkholderiaceae › Burkholderia › Burkholderia xenovorans

Protein attributes

Sequence length	277 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	Cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH.
Pathway	Xenobiotic degradation; biphenyl degradation; 2-hydroxy-2,4-pentadienoate and benzoate from biphenyl: step 2/4.
Sequence similarities	Belongs to the short-chain dehydrogenases/reductases (SDR) family.

Ontologies

Keywords
Biological process	Aromatic hydrocarbons catabolism
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	aromatic compound catabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 277

277

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

PRO_0000054531

Regions

Nucleotide binding

9 – 36

28

NAD

Sites

Active site

155

1

Proton acceptor

Binding site

59

1

NAD

Binding site

142

1

Substrate By similarity

Binding site

159

1

NAD

Secondary structure

1

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277

Helix Strand Turn

Details...

Turn

2 – 5

4

Beta strand

7 – 11

5

Turn

12 – 14

3

Helix

16 – 27

12

Beta strand

31 – 37

7

Helix

39 – 49

11

Helix

50 – 52

3

Beta strand

53 – 57

5

Helix

63 – 77

15

Beta strand

82 – 84

3

Helix

96 – 98

3

Turn

101 – 103

3

Helix

104 – 115

12

Helix

117 – 133

17

Beta strand

136 – 140

5

Helix

143 – 145

3

Helix

153 – 173

21

Turn

174 – 176

3

Beta strand

178 – 184

7

Helix

195 – 197

3

Helix

209 – 213

5

Turn

214 – 216

3

Helix

225 – 228

4

Helix

230 – 236

7

Helix

238 – 241

4

Beta strand

248 – 254

7

Helix

255 – 257

3

Helix

269 – 273

5

Sequences

	Sequence		Length	Mass (Da)
	P47227 [UniParc]. Last modified February 1, 1996. Version 1. Checksum: 00194120BD4E12D1	FASTA	277	28,901
	10 20 30 40 50 60 MKLKGEAVLI TGGASGLGRA LVDRFVAEGA KVAVLDKSAE RLAELETDHG DNVLGIVGDV 70 80 90 100 110 120 RSLEDQKQAA SRCVARFGKI DTLIPNAGIW DYSTALVDLP EESLDAAFDE VFHINVKGYI 130 140 150 160 170 180 HAVKACLPAL VASRGNVIFT ISNAGFYPNG GGPLYTAAKH AIVGLVRELA FELAPYVRVN 190 200 210 220 230 240 GVGSGGINSD LRGPSSLGMG SKAISTVPLA DMLKSVLPIG RMPEVEEYTG AYVFFATRGD 250 260 270 AAPATGALLN YDGGLGVRGF FSGAGGNDLL EQLNIHP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genetic analysis of a Pseudomonas locus encoding a pathway for biphenyl/polychlorinated biphenyl degradation." Hofer B., Eltis L.D., Dowling D.N., Timmis K.N. Gene 130:47-55(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility." Chain P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L., Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V., Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J., Parnell J.J. , Ramette A., Richardson P., Seeger M., Smith D., Spilker T., Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M. Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LB400.
[3]	"Nucleotide sequencing and transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain LB400." Erickson B.D., Mondello F.J. J. Bacteriol. 174:2903-2912(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
[4]	"Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0-A resolution." Huelsmeyer M., Hecht H.-J., Niefind K., Hofer B., Eltis L.D., Timmis K.N., Schomburg D. Protein Sci. 7:1286-1293(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH NAD.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X66122 Genomic DNA. Translation: CAA46909.1.
CP000272 Genomic DNA. Translation: ABE37054.1.
M86348 Genomic DNA. Translation: AAB63430.2.

PIR

JN0814.

RefSeq

YP_556404.1. NC_007953.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BDB	X-ray	2.00	A	1-277	[»]

ProteinModelPortal

P47227.

SMR

P47227. Positions 1-276.

ModBase

Search...

Protein-protein interaction databases

STRING

266265.Bxe_C1192.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ABE37054; ABE37054; Bxe_C1192.

GeneID

4010704.

KEGG

bxe:Bxe_C1192.

PATRIC

19343369. VBIBurXen52548_8942.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG1028.

KO

K08690.

OMA

PNAGIWD.

ProtClustDB

PRK06200.

Enzyme and pathway databases

BioCyc

BXEN266265:GJII-8844-MONOMER.

UniPathway

UPA00155; UER00251.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.

InterPro

IPR017711. BphB_TodD.
IPR002198. DH_sc/Rdtase_SDR.
IPR002347. Glc/ribitol_DH.
IPR016040. NAD(P)-bd_dom.
IPR020904. Sc_DH/Rdtase_CS.
[Graphical view]

Pfam

PF00106. adh_short. 1 hit.
[Graphical view]

PRINTS

PR00081. GDHRDH.
PR00080. SDRFAMILY.

TIGRFAMs

TIGR03325. BphB_TodD. 1 hit.

PROSITE

PS00061. ADH_SHORT. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P47227.

Entry information

Entry name

BPHB_BURXL

Accession

Primary (citable) accession number: P47227
Secondary accession number(s): Q13FT5, Q52435

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	February 1, 1996
Last modified:	May 29, 2013
This is version 104 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program