EzCatDB: D00448
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DB codeD00448
CATH domainDomain 13.10.180.10 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Domain 23.10.180.10 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1Catalytic domain
E.C.1.13.11.39

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

Enzyme Name
UniProtKBKEGG

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
RefSeq
YP_556403.1 (Protein)
NC_007953.1 (DNA/RNA sequence)
PfamPF00903 (Glyoxalase)
[Graphical view]
PF00903 (Glyoxalase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00361gamma-Hexachlorocyclohexane degradation
MAP00621Biphenyl degradation

UniProtKB: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.

Compound table: links to PDB-related databases & PoSSuM

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
ChEBI18248
82664
16205
27140
26689
15379

PubChem23925
254
977

            
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 UniProtKBP47228
[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 UniProtKBP17297
[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 UniProtKBP47228
[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 UniProtKBP17297
[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 UniProtKBP17297
[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
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
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Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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