DB code: D00448

CATH domain 3.10.180.10 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
3.10.180.10 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 Catalytic domain
E.C. 1.13.11.39
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.10.180.10 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 D00446 D00447 S00540 S00185

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
P17297 Biphenyl-2,3-diol 1,2-dioxygenase
EC 1.13.11.39
23OHBP oxygenase
2,3-dihydroxybiphenyl dioxygenase
DHBD
PF00903 (Glyoxalase)
[Graphical View]
P47228 Biphenyl-2,3-diol 1,2-dioxygenase
EC 1.13.11.39
23OHBP oxygenase
2,3-dihydroxybiphenyl dioxygenase
DHBD
PF00903 (Glyoxalase)
[Graphical View] 		YP_556403.1 (Protein)
NC_007953.1 (DNA/RNA sequence)

KEGG enzyme name
biphenyl-2,3-diol 1,2-dioxygenase
2,3-dihydroxybiphenyl dioxygenase
biphenyl-2,3-diol dioxygenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P17297 BPHC_PSES1 Biphenyl-2,3-diol + O(2) = 2-hydroxy-6-oxo-6- phenylhexa-2,4-dienoate + H(2)O. Homooctamer. Fe(2+) ion.
P47228 BPHC_BURXL Biphenyl-2,3-diol + O(2) = 2-hydroxy-6-oxo-6- phenylhexa-2,4-dienoate + H(2)O. Homooctamer. The enzyme is composed of two planar tetramers rotated at 45 degrees relative to each other, with a channel in the middle. Binds 1 Fe(2+) ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00361 gamma-Hexachlorocyclohexane degradation
MAP00621 Biphenyl degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00023 C02526 C00007 C01273
E.C.
Compound Iron Biphenyl-2,3-diol O2 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
Type heavy metal aromatic ring (only carbon atom) others aromatic ring (only carbon atom),carbohydrate,carboxyl group
ChEBI 18248
 82664
 18248
 82664
 		16205
 16205
 		15379
 26689
 27140
 15379
 26689
 27140
PubChem 23925
 23925
 		254
 254
 		977
 977
1dhyA01 Unbound Unbound Unbound Unbound
1eilA01 Unbound Unbound Unbound Unbound
1eimA01 Unbound Unbound Unbound Unbound
1eiqA01 Unbound Unbound Unbound Unbound
1eirA01 Unbound Unbound Unbound Unbound
1kw3B01 Unbound Unbound Unbound Unbound
1kw6B01 Unbound Unbound Unbound Unbound
1kw8B01 Unbound Unbound Unbound Unbound
1kw9B01 Unbound Unbound Unbound Unbound
1kwbB01 Unbound Unbound Unbound Unbound
1kwcB01 Unbound Unbound Unbound Unbound
1hanA01 Unbound Unbound Unbound Unbound
1kmyA01 Unbound Unbound Unbound Unbound
1kndA01 Unbound Unbound Unbound Unbound
1knfA01 Unbound Unbound Unbound Unbound
1lgtA01 Unbound Unbound Unbound Unbound
1lkdA01 Unbound Unbound Unbound Unbound
1dhyA02 Bound:_FE Unbound Unbound Unbound
1eilA02 Bound:_FE Unbound Unbound Unbound
1eimA02 Bound:_FE Bound:BPY Unbound Unbound
1eiqA02 Bound:_FE Unbound Unbound Unbound
1eirA02 Bound:_FE Bound:BPY Unbound Unbound
1kw3B02 Bound:FE2 Unbound Unbound Unbound
1kw6B02 Bound:FE2 Bound:BPY Unbound Unbound
1kw8B02 Bound:FE2 Bound:BPY Analogue:_NO Unbound
1kw9B02 Bound:FE2 Bound:BPY Unbound Unbound
1kwbB02 Unbound Unbound Unbound Unbound
1kwcB02 Unbound Bound:BPY Unbound Unbound
1hanA02 Bound:_FE Unbound Unbound Unbound
1kmyA02 Bound:FE2 Bound:BPY Unbound Unbound
1kndA02 Bound:FE2 Analogue:CAQ Unbound Unbound
1knfA02 Bound:FE2 Analogue:MBD Unbound Unbound
1lgtA02 Bound:FE2 Analogue:BP3_300 Unbound Unbound
1lkdA02 Bound:FE2 Analogue:BP6_300 Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dhyA01
1eilA01
1eimA01
1eiqA01
1eirA01
1kw3B01
1kw6B01
1kw8B01
1kw9B01
1kwbB01
1kwcB01
1hanA01
1kmyA01
1kndA01
1knfA01
1lgtA01
1lkdA01
1dhyA02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1eilA02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1eimA02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1eiqA02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1eirA02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kw3B02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kw6B02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kw8B02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kw9B02 HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kwbB02 HIS 194;TYR 249 ;HIS 209;GLU 260(Iron binding) mutant H145A
1kwcB02 HIS 194;TYR 249 ;HIS 209;GLU 260(Iron binding) mutant H145A
1hanA02 HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1kmyA02 HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1kndA02 HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1knfA02 HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1lgtA02 HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1lkdA02 HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
Fig.10, p.746-747
[13]
p.277-279
[14]
Fig.10, p.2495-2496
[15]
Fig.8, p.632
[18]
Fig.22, p.8923-8932

References
[1]
Resource
Comments
Medline ID
PubMed ID 8428946
Journal J Biol Chem
Year 1993
Volume 268
Pages 2727-32
Authors Eltis LD, Hofmann B, Hecht HJ, Lunsdorf H, Timmis KN
Title Purification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID
Journal Proc Jpn Acad Ser B Phys Biol Sci
Year 1995
Volume 71
Pages 32-5
Authors Sugiyama K, Senda T, Narita H, Yamamoto T, Kimbara K, Fukuda M, Yano K, Mitsui Y
Title 3-dimensional structure of 2,3-dihydroxybiphenyl dioxygenase (bphc enzyme) from pseudomonas sp strain-kks102 having polychlorinated biphenyl (pcb)-degrading activity.
Related PDB 1dhy
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7479701
Journal Proteins
Year 1995
Volume 22
Pages 284-6
Authors Sugiyama K, Narita H, Yamamoto T, Senda T, Kimbara K, Inokuchi N, Iwama M, Irie M, Fukuda M, Yano K, et al
Title Crystallization and preliminary crystallographic analysis of a 2,3-dihydroxybiphenyl dioxygenase from Pseudomonas sp. strain KKS102 having polychlorinated biphenyl (PCB)-degrading activity.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID
PubMed ID 7481800
Journal Science
Year 1995
Volume 270
Pages 976-80
Authors Han S, Eltis LD, Timmis KN, Muchmore SW, Bolin JT
Title Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad.
Related PDB 1han
Related UniProtKB P47228
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID 96226036
PubMed ID 8636975
Journal J Mol Biol
Year 1996
Volume 255
Pages 735-52
Authors Senda T, Sugiyama K, Narita H, Yamamoto T, Kimbara K, Fukuda M, Sato M, Yano K, Mitsui Y
Title 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.
Related PDB
Related UniProtKB P17297
[6]
Resource
Comments
Medline ID
PubMed ID 9603871
Journal J Bacteriol
Year 1998
Volume 180
Pages 2849-53
Authors Riegert U, Heiss G, Fischer P, Stolz A
Title Distal cleavage of 3-chlorocatechol by an extradiol dioxygenase to 3-chloro-2-hydroxymuconic semialdehyde.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID
PubMed ID 9857017
Journal J Biol Chem
Year 1998
Volume 273
Pages 34887-95
Authors Vaillancourt FH, Han S, Fortin PD, Bolin JT, Eltis LD
Title Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
Related PDB 1kmy 1knd 1knf
Related UniProtKB P47228
[8]
Resource
Comments
Medline ID
PubMed ID 10082363
Journal Protein Sci
Year 1998
Volume 7
Pages 1661-70
Authors Bergdoll M, Eltis LD, Cameron AD, Dumas P, Bolin JT
Title All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10438749
Journal J Bacteriol
Year 1999
Volume 181
Pages 4812-7
Authors Riegert U, Heiss G, Kuhm AE, Muller C, Contzen M, Knackmuss HJ, Stolz A
Title Catalytic properties of the 3-chlorocatechol-oxidizing 2, 3-dihydroxybiphenyl 1,2-dioxygenase from Sphingomonas sp. strain BN6.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10777527
Journal J Biol Chem
Year 2000
Volume 275
Pages 12430-7
Authors Imbeault NY, Powlowski JB, Colbert CL, Bolin JT, Eltis LD
Title Steady-state kinetic characterization and crystallization of a polychlorinated biphenyl-transforming dioxygenase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10900199
Journal J Biol Chem
Year 2000
Volume 275
Pages 31016-23
Authors Watanabe T, Inoue R, Kimura N, Furukawa K
Title Versatile transcription of biphenyl catabolic bph operon in Pseudomonas pseudoalcaligenes KF707.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11244073
Journal J Bacteriol
Year 2001
Volume 183
Pages 2322-30
Authors Riegert U, Burger S, Stolz A
Title Altering catalytic properties of 3-chlorocatechol-oxidizing extradiol dioxygenase from Sphingomonas xenophaga BN6 by random mutagenesis.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID
PubMed ID 11293547
Journal J Inorg Biochem
Year 2001
Volume 83
Pages 269-79
Authors Uragami Y, Senda T, Sugimoto K, Sato N, Nagarajan V, Masai E, Fukuda M, Mitsu Y
Title Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase.
Related PDB 1eil 1eiq 1eir
Related UniProtKB P17297
[14]
Resource
Comments
Medline ID
PubMed ID 11890797
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 2485-96
Authors Vaillancourt FH, Barbosa CJ, Spiro TG, Bolin JT, Blades MW, Turner RF, Eltis LD
Title Definitive evidence for monoanionic binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl 1,2-dioxygenase from UV resonance Raman spectroscopy, UV/Vis absorption spectroscopy, and crystallography.
Related PDB
Related UniProtKB
[15]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF NATIVE ENZYME, SUBSTRATE COMPLEXES, AND H145A MUTANT.
Medline ID
PubMed ID 12206778
Journal J Mol Biol
Year 2002
Volume 321
Pages 621-36
Authors Sato N, Uragami Y, Nishizaki T, Takahashi Y, Sazaki G, Sugimoto K, Nonaka T, Masai E, Fukuda M, Senda T
Title Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase.
Related PDB 1eim 1kw3 1kw6 1kw8 1kw9 1kwb 1kwc
Related UniProtKB P17297
[16]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12415290
Journal Nat Struct Biol
Year 2002
Volume 9
Pages 934-9
Authors Dai S, Vaillancourt FH, Maaroufi H, Drouin NM, Neau DB, Snieckus V, Bolin JT, Eltis LD
Title Identification and analysis of a bottleneck in PCB biodegradation.
Related PDB 1lgt 1lkd
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 12672826
Journal J Biol Chem
Year 2003
Volume 278
Pages 21483-92
Authors Hatta T, Mukerjee-Dhar G, Damborsky J, Kiyohara H, Kimbara K
Title Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 15264822
Journal J Am Chem Soc
Year 2004
Volume 126
Pages 8919-32
Authors Siegbahn PE, Haeffner F
Title Mechanism for catechol ring-cleavage by non-heme iron extradiol dioxygenases.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 15361621
Journal Science
Year 2004
Volume 305
Pages 1605-9
Authors Zhou R, Huang X, Margulis CJ, Berne BJ
Title Hydrophobic collapse in multidomain protein folding.
Related PDB
Related UniProtKB

Comments
Although a water is annotated as a product molecule in Swiss-prot database, it should not be formed as a product, in terms of chemical formulae.

Created Updated
2004-10-28 2009-02-26