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Literature summary for 1.3.1.56 extracted from
- Dynamic characterization and substrate binding of cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase - an enzyme used in bioremediation (2014), J. Mol. Model., 20, 2531 .
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| crystal structure analysis of PpBphB, PDB ID 3ZV5, overview | Pandoraea pnomenusa |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ | Pandoraea pnomenusa | - |
biphenyl-2,3-diol + NADH + H+ | - |
? |  |
| cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ | Pandoraea pnomenusa B-356 | - |
biphenyl-2,3-diol + NADH + H+ | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Pandoraea pnomenusa | - |
- |
- |
| Pandoraea pnomenusa B-356 | - |
- |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ | - |
Pandoraea pnomenusa | biphenyl-2,3-diol + NADH + H+ | - |
? | |
| cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ | - |
Pandoraea pnomenusa B-356 | biphenyl-2,3-diol + NADH + H+ | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| homodimer | 2 * 29400, functional form | Pandoraea pnomenusa |
| More | three-dimensional enzyme structure analysis, crystal structure analysis of PpBphB, PDB ID 3ZV5, molecular dynamics simulations, overview | Pandoraea pnomenusa |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| BphB | - |
Pandoraea pnomenusa |
| NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | - |
Pandoraea pnomenusa |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| NAD+ | dependent on | Pandoraea pnomenusa | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | PbBphB is a member of the short-chain dehydrogenase/reductase (SRD) family | Pandoraea pnomenusa |
| metabolism | NAD-dependent cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB) catalyzes the second step of the PCB catabolic pathway in bacteria | Pandoraea pnomenusa |
| additional information | the pocket between strand beta6 and helix alpha8 is the substrate-binding region and corresponds to a disordered region (Leu199-Ser206) in the structures of the apo and binary forms, dynamic behavior of the substrate binding loop. In the holo form, BPY stabilizes the conformation of the binding loop by interacting through the aromatic rings of reaction product 2,3-dihydroxybiphenyl with Val207 and Pro208 residues. Ile204 makes a hydrophobic interaction with the NAD+ cofactor only in the holo simulation. The lack of the latter interaction in the apo and in the binary forms explains the extended mobility of this region in the other two binding states of the protein | Pandoraea pnomenusa |
| physiological function | the enzyme is the key enzyme in the biphenyl/polychlorinated biphenyl catabolic pathway | Pandoraea pnomenusa |
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