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 |
|---|---|---|---|---|---|
| P47227 | BPHB_BURCE | Cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD(+) = biphenyl-2,3-diol + NADH. | |||
| Q46381 | BPHB_COMTE | Cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH. | Homotetramer |
| 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 32922 |
15846 15846 |
16205 16205 |
16908 16908 |
15378 15378 |
||||||
| PubChem |
5459789 5459789 |
5893 5893 |
254 254 |
439153 439153 |
1038 1038 |
||||||
| 1bdbA00 |
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Unbound | Bound:NAD | Unbound | Unbound | Unbound | |
| 2y93A00 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2y93B00 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2y99A00 |
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Unbound | Bound:NAD | Unbound | Unbound | Unbound | |
| 2y99B00 |
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Unbound | Bound:NAD | Unbound | Unbound | Unbound | |
| 3zv3A00 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3zv3B00 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3zv4A00 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3zv4B00 |
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Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3zv5A00 |
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Unbound | Bound:NAD | Bound:BPY | Unbound | Unbound | |
| 3zv5B00 |
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Unbound | Bound:NAD | Unbound | Unbound | Unbound | |
| 3zv6A00 |
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Unbound | Bound:NAD | Analogue:4HB | Unbound | Unbound | |
| 3zv6B00 |
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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 |
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SER 142;TYR 155;LYS 159 | ||||
| 2y93A00 |
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SER 142;TYR 155;LYS 159 | ||||
| 2y93B00 |
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SER 142;TYR 155;LYS 159 | ||||
| 2y99A00 |
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SER 142;TYR 155;LYS 159 | ||||
| 2y99B00 |
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SER 142;TYR 155;LYS 159 | ||||
| 3zv3A00 |
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SER 142;TYR 155;LYS 159 | ||||
| 3zv3B00 |
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SER 142;TYR 155;LYS 159 | ||||
| 3zv4A00 |
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SER 142;TYR 155;LYS 159 | ||||
| 3zv4B00 |
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SER 142;TYR 155;LYS 159 | ||||
| 3zv5A00 |
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SER 142;TYR 155;LYS 159 | ||||
| 3zv5B00 |
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SER 142;TYR 155;LYS 159 | ||||
| 3zv6A00 |
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SER 142;TYR 155;LYS 159 | ||||
| 3zv6B00 |
|
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|
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 |
|---|
|
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, According to the literature [3], (A) Hydride transfer from 1-hydroxyl-carbon atom of biphenyl-1,2-diol to nicotinamide of NAD, 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]). |
| Created | Updated |
|---|---|
| 2012-09-25 | 2012-10-04 |