EzCatDB: D00448

DB codeD00448
CATH domainDomain 13.10.180.10
Domain 23.10.180.10Catalytic domain
E.C.1.13.11.39

CATH domainRelated DB codes (homologues)
3.10.180.10D00446,D00447,S00540,S00185

Enzyme Name
Swiss-protKEGG

P17297P47228
Protein nameBiphenyl-2,3-diol 1,2-dioxygenaseBiphenyl-2,3-diol 1,2-dioxygenasebiphenyl-2,3-diol 1,2-dioxygenase
2,3-dihydroxybiphenyl dioxygenase
biphenyl-2,3-diol dioxygenase
SynonymsEC 1.13.11.39
23OHBP oxygenase
2,3-dihydroxybiphenyl dioxygenase
DHBD
EC 1.13.11.39
23OHBP oxygenase
2,3-dihydroxybiphenyl dioxygenase
DHBD

KEGG pathways
MAP codePathways
MAP00361gamma-Hexachlorocyclohexane degradation
MAP00621Biphenyl degradation

Swiss-prot:Accession NumberP17297P47228
Entry nameBPHC_PSES1BPHC_BURXL
ActivityBiphenyl-2,3-diol + O(2) = 2-hydroxy-6-oxo-6- phenylhexa-2,4-dienoate + H(2)O.Biphenyl-2,3-diol + O(2) = 2-hydroxy-6-oxo-6- phenylhexa-2,4-dienoate + H(2)O.
SubunitHomooctamer.Homooctamer. The enzyme is composed of two planar tetramers rotated at 45 degrees relative to each other, with a channel in the middle.
Subcellular location

CofactorFe(2+) ion.Binds 1 Fe(2+) ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00023C02526C00007C01273
CompoundIronBiphenyl-2,3-diolO22-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
Typeheavy metalaromatic ring (only carbon atom)othersaromatic ring (only carbon atom),carbohydrate,carboxyl group
1dhyA01UnboundUnboundUnboundUnbound
1eilA01UnboundUnboundUnboundUnbound
1eimA01UnboundUnboundUnboundUnbound
1eiqA01UnboundUnboundUnboundUnbound
1eirA01UnboundUnboundUnboundUnbound
1kw3B01UnboundUnboundUnboundUnbound
1kw6B01UnboundUnboundUnboundUnbound
1kw8B01UnboundUnboundUnboundUnbound
1kw9B01UnboundUnboundUnboundUnbound
1kwbB01UnboundUnboundUnboundUnbound
1kwcB01UnboundUnboundUnboundUnbound
1hanA01UnboundUnboundUnboundUnbound
1kmyA01UnboundUnboundUnboundUnbound
1kndA01UnboundUnboundUnboundUnbound
1knfA01UnboundUnboundUnboundUnbound
1lgtA01UnboundUnboundUnboundUnbound
1lkdA01UnboundUnboundUnboundUnbound
1dhyA02Bound:_FEUnboundUnboundUnbound
1eilA02Bound:_FEUnboundUnboundUnbound
1eimA02Bound:_FEBound:BPYUnboundUnbound
1eiqA02Bound:_FEUnboundUnboundUnbound
1eirA02Bound:_FEBound:BPYUnboundUnbound
1kw3B02Bound:FE2UnboundUnboundUnbound
1kw6B02Bound:FE2Bound:BPYUnboundUnbound
1kw8B02Bound:FE2Bound:BPYAnalogue:_NOUnbound
1kw9B02Bound:FE2Bound:BPYUnboundUnbound
1kwbB02UnboundUnboundUnboundUnbound
1kwcB02UnboundBound:BPYUnboundUnbound
1hanA02Bound:_FEUnboundUnboundUnbound
1kmyA02Bound:FE2Bound:BPYUnboundUnbound
1kndA02Bound:FE2Analogue:CAQUnboundUnbound
1knfA02Bound:FE2Analogue:MBDUnboundUnbound
1lgtA02Bound:FE2Analogue:BP3 300UnboundUnbound
1lkdA02Bound:FE2Analogue:BP6 300UnboundUnbound

Active-site residues
resource
literature [5]
pdbCatalytic residuesCofactor-binding residuescomment
1dhyA01


1eilA01


1eimA01


1eiqA01


1eirA01


1kw3B01


1kw6B01


1kw8B01


1kw9B01


1kwbB01


1kwcB01


1hanA01


1kmyA01


1kndA01


1knfA01


1lgtA01


1lkdA01


1dhyA02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1eilA02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1eimA02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1eiqA02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1eirA02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1kw3B02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1kw6B02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1kw8B02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1kw9B02HIS 194;TYR 249
HIS 145;HIS 209;GLU 260(Iron binding)

1kwbB02HIS 194;TYR 249
       ;HIS 209;GLU 260(Iron binding)
mutant H145A
1kwcB02HIS 194;TYR 249
       ;HIS 209;GLU 260(Iron binding)
mutant H145A
1hanA02HIS 195;TYR 250
HIS 146;HIS 210;GLU 260(Iron binding)

1kmyA02HIS 195;TYR 250
HIS 146;HIS 210;GLU 260(Iron binding)

1kndA02HIS 195;TYR 250
HIS 146;HIS 210;GLU 260(Iron binding)

1knfA02HIS 195;TYR 250
HIS 146;HIS 210;GLU 260(Iron binding)

1lgtA02HIS 195;TYR 250
HIS 146;HIS 210;GLU 260(Iron binding)

1lkdA02HIS 195;TYR 250
HIS 146;HIS 210;GLU 260(Iron binding)


References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID8428946
JournalJ Biol Chem
Year1993
Volume268
Pages2727-32
AuthorsEltis LD, Hofmann B, Hecht HJ, Lunsdorf H, Timmis KN
TitlePurification and crystallization of 2,3-dihydroxybiphenyl 1,2-dioxygenase.
[2]
CommentsX-ray crystallography
JournalProc Jpn Acad Ser B Phys Biol Sci
Year1995
Volume71
Pages32-5
AuthorsSugiyama K, Senda T, Narita H, Yamamoto T, Kimbara K, Fukuda M, Yano K, Mitsui Y
Title3-dimensional structure of 2,3-dihydroxybiphenyl dioxygenase (bphc enzyme) from pseudomonas sp strain-kks102 having polychlorinated biphenyl (pcb)-degrading activity.
Related PDB1dhy
[3]
PubMed ID7479701
JournalProteins
Year1995
Volume22
Pages284-6
AuthorsSugiyama K, Narita H, Yamamoto T, Senda T, Kimbara K, Inokuchi N, Iwama M, Irie M, Fukuda M, Yano K, et al
TitleCrystallization and preliminary crystallographic analysis of a 2,3-dihydroxybiphenyl dioxygenase from Pseudomonas sp. strain KKS102 having polychlorinated biphenyl (PCB)-degrading activity.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
PubMed ID7481800
JournalScience
Year1995
Volume270
Pages976-80
AuthorsHan S, Eltis LD, Timmis KN, Muchmore SW, Bolin JT
TitleCrystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad.
Related PDB1han
Related Swiss-protP47228
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID96226036
PubMed ID8636975
JournalJ Mol Biol
Year1996
Volume255
Pages735-52
AuthorsSenda T, Sugiyama K, Narita H, Yamamoto T, Kimbara K, Fukuda M, Sato M, Yano K, Mitsui Y
TitleThree-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 Swiss-protP17297
[6]
PubMed ID9603871
JournalJ Bacteriol
Year1998
Volume180
Pages2849-53
AuthorsRiegert U, Heiss G, Fischer P, Stolz A
TitleDistal cleavage of 3-chlorocatechol by an extradiol dioxygenase to 3-chloro-2-hydroxymuconic semialdehyde.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
PubMed ID9857017
JournalJ Biol Chem
Year1998
Volume273
Pages34887-95
AuthorsVaillancourt FH, Han S, Fortin PD, Bolin JT, Eltis LD
TitleMolecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
Related PDB1kmy,1knd,1knf
Related Swiss-protP47228
[8]
PubMed ID10082363
JournalProtein Sci
Year1998
Volume7
Pages1661-70
AuthorsBergdoll M, Eltis LD, Cameron AD, Dumas P, Bolin JT
TitleAll in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly.
[9]
PubMed ID10438749
JournalJ Bacteriol
Year1999
Volume181
Pages4812-7
AuthorsRiegert U, Heiss G, Kuhm AE, Muller C, Contzen M, Knackmuss HJ, Stolz A
TitleCatalytic properties of the 3-chlorocatechol-oxidizing 2, 3-dihydroxybiphenyl 1,2-dioxygenase from Sphingomonas sp. strain BN6.
[10]
PubMed ID10777527
JournalJ Biol Chem
Year2000
Volume275
Pages12430-7
AuthorsImbeault NY, Powlowski JB, Colbert CL, Bolin JT, Eltis LD
TitleSteady-state kinetic characterization and crystallization of a polychlorinated biphenyl-transforming dioxygenase.
[11]
PubMed ID10900199
JournalJ Biol Chem
Year2000
Volume275
Pages31016-23
AuthorsWatanabe T, Inoue R, Kimura N, Furukawa K
TitleVersatile transcription of biphenyl catabolic bph operon in Pseudomonas pseudoalcaligenes KF707.
[12]
PubMed ID11244073
JournalJ Bacteriol
Year2001
Volume183
Pages2322-30
AuthorsRiegert U, Burger S, Stolz A
TitleAltering catalytic properties of 3-chlorocatechol-oxidizing extradiol dioxygenase from Sphingomonas xenophaga BN6 by random mutagenesis.
[13]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
PubMed ID11293547
JournalJ Inorg Biochem
Year2001
Volume83
Pages269-79
AuthorsUragami Y, Senda T, Sugimoto K, Sato N, Nagarajan V, Masai E, Fukuda M, Mitsu Y
TitleCrystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase.
Related PDB1eil,1eiq,1eir
Related Swiss-protP17297
[14]
PubMed ID11890797
JournalJ Am Chem Soc
Year2002
Volume124
Pages2485-96
AuthorsVaillancourt FH, Barbosa CJ, Spiro TG, Bolin JT, Blades MW, Turner RF, Eltis LD
TitleDefinitive 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.
[15]
CommentsX-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF NATIVE ENZYME, SUBSTRATE COMPLEXES, AND H145A MUTANT.
PubMed ID12206778
JournalJ Mol Biol
Year2002
Volume321
Pages621-36
AuthorsSato N, Uragami Y, Nishizaki T, Takahashi Y, Sazaki G, Sugimoto K, Nonaka T, Masai E, Fukuda M, Senda T
TitleCrystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase.
Related PDB1eim,1kw3,1kw6,1kw8,1kw9,1kwb,1kwc
Related Swiss-protP17297
[16]
CommentsX-ray crystallography
PubMed ID12415290
JournalNat Struct Biol
Year2002
Volume9
Pages934-9
AuthorsDai S, Vaillancourt FH, Maaroufi H, Drouin NM, Neau DB, Snieckus V, Bolin JT, Eltis LD
TitleIdentification and analysis of a bottleneck in PCB biodegradation.
Related PDB1lgt,1lkd
[17]
PubMed ID12672826
JournalJ Biol Chem
Year2003
Volume278
Pages21483-92
AuthorsHatta T, Mukerjee-Dhar G, Damborsky J, Kiyohara H, Kimbara K
TitleCharacterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8.
[18]
PubMed ID15264822
JournalJ Am Chem Soc
Year2004
Volume126
Pages8919-32
AuthorsSiegbahn PE, Haeffner F
TitleMechanism for catechol ring-cleavage by non-heme iron extradiol dioxygenases.
[19]
PubMed ID15361621
JournalScience
Year2004
Volume305
Pages1605-9
AuthorsZhou R, Huang X, Margulis CJ, Berne BJ
TitleHydrophobic collapse in multidomain protein folding.

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.

createdupdated
2004-10-282009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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