Reviewed, UniProtKB/Swiss-Prot P17297 (BPHC_PSES1)

Names and origin

Protein names

Recommended name:
    Biphenyl-2,3-diol 1,2-dioxygenase
    EC=1.13.11.39
Alternative name(s):
    23OHBP oxygenase
    2,3-dihydroxybiphenyl dioxygenase
      Short name=DHBD

Gene names

Name:

bphC

Organism

Pseudomonas sp. (strain KKS102)

Taxonomic identifier

307 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria

Protein attributes

Sequence length	293 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	Biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H2O.
Cofactor	Fe2+ ion.
Pathway	Xenobiotic degradation; biphenyl degradation; 2-hydroxy-2,4-pentadienoic acid and benzoic acid from biphenyl: step 3/4.
Subunit structure	Homooctamer.
Sequence similarities	Belongs to the extradiol ring-cleavage dioxygenase family.

Ontologies

Keywords
Biological process	Aromatic hydrocarbons catabolism
Ligand	Iron Metal-binding
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	aromatic compound catabolic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW xenobiotic catabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	biphenyl-2,3-diol 1,2-dioxygenase activity Inferred from electronic annotation. Source: EC ferrous iron binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 293

292

Biphenyl-2,3-diol 1,2-dioxygenase

PRO_0000085035

Sites

Metal binding

146

1

Iron

Metal binding

210

1

Iron

Metal binding

261

1

Iron

Secondary structure

1

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293

Helix Strand Turn

Details...

Beta strand

5 – 14

10

Helix

16 – 25

10

Beta strand

30 – 35

6

Beta strand

38 – 47

10

Beta strand

49 – 54

6

Beta strand

59 – 66

8

Helix

70 – 83

14

Helix

92 – 98

7

Beta strand

101 – 107

7

Beta strand

113 – 118

6

Beta strand

131 – 133

3

Helix

140 – 142

3

Beta strand

146 – 150

5

Helix

154 – 163

10

Beta strand

168 – 178

11

Beta strand

181 – 194

14

Beta strand

196 – 200

5

Beta strand

205 – 217

13

Helix

218 – 230

13

Beta strand

238 – 244

7

Beta strand

247 – 252

6

Beta strand

259 – 264

6

Beta strand

277 – 279

3

Beta strand

281 – 285

5

Sequences

	Sequence		Length	Mass (Da)
	P17297-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 53EF1B24502E3B24	FASTA	293	32,245
	10 20 30 40 50 60 MSIERLGYLG FAVKDVPAWD HFLTKSVGLM AAGSAGDAAL YRADQRAWRI AVQPGELDDL 70 80 90 100 110 120 AYAGLEVDDA AALERMADKL RQAGVAFTRG DEALMQQRKV MGLLCLQDPF GLPLEIYYGP 130 140 150 160 170 180 AEIFHEPFLP SAPVSGFVTG DQGIGHFVRC VPDTAKAMAF YTEVLGFVLS DIIDIQMGPE 190 200 210 220 230 240 TSVPAHFLHC NGRHHTIALA AFPIPKRIHH FMLQANTIDD VGYAFDRLDA AGRITSLLGR 250 260 270 280 290 HTNDQTLSFY ADTPSPMIEV EFGWGPRTVD SSWTVARHSR TAMWGHKSVR GQR

References

[1]	"Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium Pseudomonas sp. strain KKS102." Kimbara K., Hashimoto T., Fukuda M., Koana T., Takagi M., Oishi M., Yano K. J. Bacteriol. 171:2740-2747(1989) [PubMed: 2540155] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Identification of the bphA and bphB genes of Pseudomonas sp. strains KKS102 involved in degradation of biphenyl and polychlorinated biphenyls." Fukuda M., Yasukochi Y., Kikuchi Y., Nagata Y., Kimbara K., Horiuchi H., Takagi M., Yano K. Biochem. Biophys. Res. Commun. 202:850-856(1994) [PubMed: 8048958] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-16.
[3]	"Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102." Senda T., Sugiyama K., Narita H., Yamamoto T., Kimbara K., Fukuda M., Sato M., Yano K., Mitsui Y. J. Mol. Biol. 255:735-752(1996) [PubMed: 8636975] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[4]	"Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase." Uragami Y., Senda T., Sugimoto K., Sato N., Nagarajan V., Masai E., Fukuda M., Mitsui Y. J. Inorg. Biochem. 83:269-279(2001) [PubMed: 11293547] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[5]	"Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase." Sato N., Uragami Y., Nishizaki T., Takahashi Y., Sazaki G., Sugimoto K., Nonaka T., Masai E., Fukuda M., Senda T. J. Mol. Biol. 321:621-636(2002) [PubMed: 12206778] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF NATIVE ENZYME; SUBSTRATE COMPLEXES AND H145A MUTANT.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M26433 Genomic DNA. Translation: AAA25750.1.
D17319 Genomic DNA. Translation: BAA04141.1.

PIR

DAPSPC. A32312.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DHY	X-ray	2.30	A	2-293	[»]
1EIL	X-ray	2.00	A	2-293	[»]
1EIQ	X-ray	2.00	A	2-293	[»]
1EIR	X-ray	2.00	A	2-293	[»]
1KW3	X-ray	1.45	B	2-293	[»]
1KW6	X-ray	1.45	B	2-293	[»]
1KW8	X-ray	2.00	B	2-293	[»]
1KW9	X-ray	1.95	B	2-293	[»]
1KWB	X-ray	2.00	B	2-293	[»]
1KWC	X-ray	2.10	B	2-293	[»]

ModBase

Search...

Family and domain databases

InterPro

IPR017626. DiOHbiphenyl_dOase.
IPR004360. Glyas_bleo-R_dOase.
IPR000486. Xdiol_dOase_1_2.
[Graphical view]

Pfam

PF00903. Glyoxalase. 2 hits.
[Graphical view]

ProDom

PD002334. Gly_diox. 2 hits.
PD000977. Xdiol_dioxygnse. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR03213. 23dbph12diox. 1 hit.

PROSITE

PS00082. EXTRADIOL_DIOXYGENAS. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

BPHC_PSES1

Accession

Primary (citable) accession number: P17297
Secondary accession number(s): Q52441

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 78 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)