DB code: S00625

RLCP classification 9.1050.440000.8010 : Hydride transfer
CATH domain 3.40.50.720 : Rossmann fold Catalytic domain
E.C. 1.3.1.56
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.720 : Rossmann fold S00543 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P47227 Cis-2,3-dihydrobiphenyl-2,3-diol 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
YP_556404.1 (Protein)
NC_007953.1 (DNA/RNA sequence)
PF00106 (adh_short)
[Graphical View]
Q46381 Cis-2,3-dihydrobiphenyl-2,3-diol 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
PF00106 (adh_short)
[Graphical View]

KEGG enzyme name
cis-2,3-Dihydrobiphenyl-2,3-diol dehydrogenase
2,3-Dihydro-2,3-dihydroxybiphenyl dehydrogenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q46381 BPHB_COMTE Cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH. Homotetramer
P47227 BPHB_BURCE Cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD(+) = biphenyl-2,3-diol + NADH.

KEGG Pathways
Map code Pathways E.C.
MAP00621 Biphenyl degradation

Compound table
Substrates Products Intermediates
KEGG-id C06589 C00003 C02526 C00004 C00080 I00146
E.C.
Compound cis-3-phenylcyclohexa-3,5-diene-1,2-diol NAD+ biphenyl-2,3-diol NADH H+ 3-phenyl-2-hydroxy-cyclohexa-3,5-dienone
Type aromatic ring (only carbon atom),carbohydrate amide group,amine group,nucleotide aromatic ring (only carbon atom) amide group,amine group,nucleotide others
ChEBI 32922
15846
16205
16908
15378
PubChem 5459789
5893
254
439153
1038
1bdbA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound
2y93A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2y93B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2y99A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound
2y99B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound
3zv3A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3zv3B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3zv4A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3zv4B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3zv5A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Bound:BPY Unbound Unbound
3zv5B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound
3zv6A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Analogue:4HB Unbound Unbound
3zv6B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAD Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature[3],[4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bdbA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
2y93A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
2y93B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
2y99A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
2y99B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
3zv3A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
3zv3B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
3zv4A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
3zv4B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
3zv5A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
3zv5B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
3zv6A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159
3zv6B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 142;TYR 155;LYS 159

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
Fig.7, p.1291
[4]
p.5033

References
[1]
Resource
Comments
Medline ID
PubMed ID 8626504
Journal J Biol Chem
Year 1996
Volume 271
Pages 8152-6
Authors Hurtubise Y, Barriault D, Sylvestre M
Title Characterization of active recombinant his-tagged oxygenase component of Comamonas testosteroni B-356 biphenyl dioxygenase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9811638
Journal J Bacteriol
Year 1998
Volume 180
Pages 5828-35
Authors Hurtubise Y, Barriault D, Sylvestre M
Title Involvement of the terminal oxygenase beta subunit in the biphenyl dioxygenase reactivity pattern toward chlorobiphenyls.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9655331
Journal Protein Sci
Year 1998
Volume 7
Pages 1286-93
Authors Hulsmeyer M, Hecht HJ, Niefind K, Hofer B, Eltis LD, Timmis KN, Schomburg D
Title Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution.
Related PDB 1bdb
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 10819967
Journal Biochemistry
Year 2000
Volume 39
Pages 5028-34
Authors Vedadi M, Barriault D, Sylvestre M, Powlowski J
Title Active site residues of cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase from Comamonas testosteroni strain B-356.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 21880718
Journal J Biol Chem
Year 2011
Volume 286
Pages 37011-22
Authors Dhindwal S, Patil DN, Mohammadi M, Sylvestre M, Tomar S, Kumar P
Title Biochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme.
Related PDB 2y93 2y99 3zv3 3zv4 3zv5 3zv6
Related UniProtKB

Comments
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]).
This enzyme belongs to the short-chain dehydrogenase/reductase (SDR) superfamily.

Created Updated
2012-09-25 2012-10-04