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
2,3-dihydroxybiphenyl dioxygenase
DHBD
23OHBP oxygenase
PF00903 (Glyoxalase)
[Graphical View]
P47228 Biphenyl-2,3-diol 1,2-dioxygenase
EC 1.13.11.39
2,3-dihydroxybiphenyl dioxygenase
DHBD
23OHBP oxygenase
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
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.
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.

KEGG Pathways
Map code Pathways E.C.
MAP00621 Biphenyl degradation
MAP00361 gamma-Hexachlorocyclohexane 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
16205
15379
26689
27140
PubChem 23925
254
977
1dhyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eilA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eimA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eiqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eirA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kw3B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kw6B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kw8B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kw9B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kwbB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kwcB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1hanA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kmyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kndA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1knfA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1lgtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1lkdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1dhyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound
1eilA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound
1eimA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:BPY Unbound Unbound
1eiqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound
1eirA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:BPY Unbound Unbound
1kw3B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Unbound Unbound Unbound
1kw6B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Bound:BPY Unbound Unbound
1kw8B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Bound:BPY Analogue:_NO Unbound
1kw9B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Bound:BPY Unbound Unbound
1kwbB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1kwcB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:BPY Unbound Unbound
1hanA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Unbound Unbound Unbound
1kmyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Bound:BPY Unbound Unbound
1kndA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Analogue:CAQ Unbound Unbound
1knfA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Analogue:MBD Unbound Unbound
1lgtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Analogue:BP3_300 Unbound Unbound
1lkdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eilA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eimA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eiqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eirA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kw3B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kw6B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kw8B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kw9B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kwbB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kwcB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hanA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kmyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kndA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1knfA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1lgtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1lkdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dhyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1eilA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1eimA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1eiqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1eirA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kw3B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kw6B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kw8B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kw9B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 HIS 145;HIS 209;GLU 260(Iron binding)
1kwbB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 ;HIS 209;GLU 260(Iron binding) mutant H145A
1kwcB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 194;TYR 249 ;HIS 209;GLU 260(Iron binding) mutant H145A
1hanA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1kmyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1kndA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1knfA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1lgtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 195;TYR 250 HIS 146;HIS 210;GLU 260(Iron binding)
1lkdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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