EzCatDB: S00625
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DB codeS00625
RLCP classification9.1050.440000.8010 : Hydride transfer
CATH domainDomain 13.40.50.720 : Rossmann foldCatalytic domain
E.C.1.3.1.56

CATH domainRelated DB codes (homologues)
3.40.50.720 : Rossmann foldS00543,S00551,S00552,S00553,S00602,S00604,S00605,S00608,S00610,S00319,S00328,S00329,S00330,S00331,S00332,D00456,D00457,D00458,S00324,S00320,S00325,S00326,S00327,D00459,S00335,S00336,S00334,T00219,S00339,D00513,D00001,D00002,D00003,D00005,D00007,D00008,D00010,D00012,D00017,D00018,D00023,D00027,D00028,D00031,D00032,D00033,D00034,D00035,D00037,D00048,D00071,D00476,D00481,D00482,D00490,D00492,D00494,D00545,D00601,D00603,D00604,D00605,D00615,D00845,D00857,D00858,M00161,M00171,M00210,T00002,T00010,T00011,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
UniProtKBKEGG

P47227Q46381
Protein nameCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenaseCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenasecis-2,3-Dihydrobiphenyl-2,3-diol dehydrogenase
2,3-Dihydro-2,3-dihydroxybiphenyl dehydrogenase
SynonymsEC 1.3.1.56
Biphenyl-2,3-dihydro-2,3-diol dehydrogenase
Biphenyl-cis-diol dehydrogenase
2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase
2,3-dihydroxy-4-phenylhexa-4,6-diene dehydrogenase
EC 1.3.1.56
Biphenyl-2,3-dihydro-2,3-diol dehydrogenase
Biphenyl-cis-diol dehydrogenase
2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase
2,3-dihydroxy-4-phenylhexa-4,6-diene dehydrogenase
B2,3D
RefSeqYP_556404.1 (Protein)
NC_007953.1 (DNA/RNA sequence)

PfamPF00106 (adh_short)
[Graphical view]
PF00106 (adh_short)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00621Biphenyl degradation

UniProtKB:Accession NumberP47227Q46381
Entry nameBPHB_BURCEBPHB_COMTE
ActivityCis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD(+) = biphenyl-2,3-diol + NADH.Cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH.
Subunit
Homotetramer
Subcellular location

Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC06589C00003C02526C00004C00080I00146
Compoundcis-3-phenylcyclohexa-3,5-diene-1,2-diolNAD+biphenyl-2,3-diolNADHH+3-phenyl-2-hydroxy-cyclohexa-3,5-dienone
Typearomatic ring (only carbon atom),carbohydrateamide group,amine group,nucleotidearomatic ring (only carbon atom)amide group,amine group,nucleotideothers
ChEBI32922
15846
16205
16908
15378

PubChem5459789
5893
254
439153
1038

              
1bdbA00UnboundBound:NADUnboundUnbound Unbound
2y93A00UnboundUnboundUnboundUnbound Unbound
2y93B00UnboundUnboundUnboundUnbound Unbound
2y99A00UnboundBound:NADUnboundUnbound Unbound
2y99B00UnboundBound:NADUnboundUnbound Unbound
3zv3A00UnboundUnboundUnboundUnbound Unbound
3zv3B00UnboundUnboundUnboundUnbound Unbound
3zv4A00UnboundUnboundUnboundUnbound Unbound
3zv4B00UnboundUnboundUnboundUnbound Unbound
3zv5A00UnboundBound:NADBound:BPYUnbound Unbound
3zv5B00UnboundBound:NADUnboundUnbound Unbound
3zv6A00UnboundBound:NADAnalogue:4HBUnbound Unbound
3zv6B00UnboundBound:NADUnboundUnbound Unbound

Active-site residues
resource
literature[3],[4]
pdbCatalytic residues
         
1bdbA00SER 142;TYR 155;LYS 159
2y93A00SER 142;TYR 155;LYS 159
2y93B00SER 142;TYR 155;LYS 159
2y99A00SER 142;TYR 155;LYS 159
2y99B00SER 142;TYR 155;LYS 159
3zv3A00SER 142;TYR 155;LYS 159
3zv3B00SER 142;TYR 155;LYS 159
3zv4A00SER 142;TYR 155;LYS 159
3zv4B00SER 142;TYR 155;LYS 159
3zv5A00SER 142;TYR 155;LYS 159
3zv5B00SER 142;TYR 155;LYS 159
3zv6A00SER 142;TYR 155;LYS 159
3zv6B00SER 142;TYR 155;LYS 159

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Fig.7, p.1291
[4]p.5033

references
[1]
PubMed ID8626504
JournalJ Biol Chem
Year1996
Volume271
Pages8152-6
AuthorsHurtubise Y, Barriault D, Sylvestre M
TitleCharacterization of active recombinant his-tagged oxygenase component of Comamonas testosteroni B-356 biphenyl dioxygenase.
[2]
PubMed ID9811638
JournalJ Bacteriol
Year1998
Volume180
Pages5828-35
AuthorsHurtubise Y, Barriault D, Sylvestre M
TitleInvolvement of the terminal oxygenase beta subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls.
[3]
PubMed ID9655331
JournalProtein Sci
Year1998
Volume7
Pages1286-93
AuthorsHulsmeyer M, Hecht HJ, Niefind K, Hofer B, Eltis LD, Timmis KN, Schomburg D
TitleCrystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution.
Related PDB1bdb
[4]
PubMed ID10819967
JournalBiochemistry
Year2000
Volume39
Pages5028-34
AuthorsVedadi M, Barriault D, Sylvestre M, Powlowski J
TitleActive site residues of cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase from Comamonas testosteroni strain B-356.
[5]
PubMed ID21880718
JournalJ Biol Chem
Year2011
Volume286
Pages37011-22
AuthorsDhindwal S, Patil DN, Mohammadi M, Sylvestre M, Tomar S, Kumar P
TitleBiochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme.
Related PDB2y93,2y99,3zv3,3zv4,3zv5,3zv6

comments
This enzyme belongs to the short-chain dehydrogenase/reductase (SDR) superfamily.
Since the active site is the same as those of the homologous enzymes (S00320, S00327, S00328, S00330, S00332, S00602, S00604, S00605, S00608 and S00610 in EzCatDB), this enzyme must catalyzes the same reaction as those homologues.
According to the literature [3], this enzyme catalyzes the following reactions:
(A) Hydride transfer from 1-hydroxyl-carbon atom of biphenyl-1,2-diol to nicotinamide of NAD, forming a keto intermediate (I00146):
This reaction step seems to be the same as those homologous enzymes.
(B) Isomerization of the keto intermediate to product (keto-enol tautomerization):
This reaction step can be non-enzymatic spontaneous reaction (see [3]).

createdupdated
2012-09-252012-10-04


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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)
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 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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