Reviewed, UniProtKB/Swiss-Prot P47228 (BPHC_BURXL)

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
Ordered Locus Names:	Bxeno_C1125
ORF Names:	Bxe_C1191

Organism

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

Taxonomic identifier

266265 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Burkholderiaceae › Burkholderia

Protein attributes

Sequence length	298 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)

Function	Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.
Catalytic activity	Biphenyl-2,3-diol + O(2) = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate + H(2)O.
Cofactor	Binds 1 Fe(2+) ion per subunit.
Pathway	Xenobiotic degradation; biphenyl degradation; 2-hydroxy-2,4-pentadienoic acid and benzoic acid from biphenyl: step 3/4.
Subunit structure	Homooctamer. The enzyme is composed of two planar tetramers rotated at 45 degrees relative to each other, with a channel in the middle.
Sequence similarities	Belongs to the extradiol ring-cleavage dioxygenase family.
Biophysicochemical properties	Kinetic parameters: Substrate inhibition occurs at 300 µM (+/- 20 µM). KM=7 µM for biphenyl-2,3-diol pH dependence: Optimum pH is 8.0.

Ontologies

Keywords
Biological process	Aromatic hydrocarbons catabolism
Ligand	Iron Metal-binding
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
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 – 298

297

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

PRO_0000085033

Sites

Metal binding

146

1

Iron

Metal binding

210

1

Iron

Metal binding

260

1

Iron

Secondary structure

1

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298

Helix Strand Turn

Details...

Beta strand

3 – 14

12

Helix

16 – 25

10

Beta strand

30 – 35

6

Beta strand

38 – 47

10

Beta strand

49 – 54

6

Beta strand

59 – 69

11

Helix

70 – 82

13

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 – 176

9

Beta strand

178 – 180

3

Beta strand

182 – 194

13

Beta strand

196 – 200

5

Beta strand

205 – 217

13

Helix

218 – 229

12

Turn

230 – 232

3

Beta strand

234 – 244

11

Beta strand

247 – 252

6

Beta strand

258 – 263

6

Beta strand

275 – 278

4

Beta strand

280 – 284

5

Sequences

	Sequence		Length	Mass (Da)
	P47228-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: ADC0E4709E193FAB	FASTA	298	32,471
	10 20 30 40 50 60 MSIRSLGYMG FAVSDVAAWR SFLTQKLGLM EAGTTDNGDL FRIDSRAWRI AVQQGEVDDL 70 80 90 100 110 120 AFAGYEVADA AGLAQMADKL KQAGIAVTTG DASLARRRGV TGLITFADPF GLPLEIYYGA 130 140 150 160 170 180 SEVFEKPFLP GAAVSGFLTG EQGLGHFVRC VPDSDKALAF YTDVLGFQLS DVIDMKMGPD 190 200 210 220 230 240 VTVPAYFLHC NERHHTLAIA AFPLPKRIHH FMLEVASLDD VGFAFDRVDA DGLITSTLGR 250 260 270 280 290 HTNDHMVSFY ASTPSGVEVE YGWSARTVDR SWVVVRHDSP SMWGHKSVRD KAAARNKA

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: 8344527] [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: 17030797] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase." Eltis L.D., Hofmann B., Hecht H.J., Luensdorf H., Timmis K.N. J. Biol. Chem. 268:2727-2732(1993) [PubMed: 8428946] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-32, SUBSTRATE CHARACTERIZATION, PRELIMINARY CRYSTALLIZATION, SUBUNIT.
[4]	"Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad." Han S., Eltis L.D., Timmis K.N., Muchmore S.W., Bolin J.T. Science 270:976-980(1995) [PubMed: 7481800] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[5]	"Molecular basis for the stabilization and inhibition of 2,3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol." Vaillancourt F.H., Han S., Fortin P.D., Bolin J.T., Eltis L.D. J. Biol. Chem. 273:34887-34895(1998) [PubMed: 9857017] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X66122 Genomic DNA. Translation: CAA46910.1.
CP000272 Genomic DNA. Translation: ABE37053.1.

PIR

JN0815.

RefSeq

YP_556403.1.

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HAN	X-ray	1.90	A	1-298	[»]
1KMY	X-ray	2.00	A	1-298	[»]
1KND	X-ray	1.90	A	1-298	[»]
1KNF	X-ray	1.90	A	1-298	[»]
1LGT	X-ray	1.70	A	1-298	[»]
1LKD	X-ray	1.70	A	1-298	[»]

ModBase

Search...

Genome annotation databases

GeneID

4010703.

GenomeReviews

Gene locus Bxeno_C1125 in contig CP000272_GR.

KEGG

bxe:Bxe_C1191.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

P47228.

Enzyme and pathway databases

BioCyc

BXEN266265:BXE_C1191-MON.

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.
[Graphical view] [Entries sharing at least one domain]

PROSITE

PS00082. EXTRADIOL_DIOXYGENAS. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

LinkHub

P47228.

Entry information

Entry name

BPHC_BURXL

Accession

Primary (citable) accession number: P47228
Secondary accession number(s): Q13FT6

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	January 23, 2007
Last modified:	November 25, 2008
This is version 72 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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