Activating Compound | Comment | Organism | Structure |
---|---|---|---|
amicyanin | - |
Paracoccus denitrificans |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
methylamine + H2O + 2 amicyanin | Paracoccus denitrificans | - |
formaldehyde + NH3 + 2 reduced amicyanin | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Paracoccus denitrificans | P22619 AND P29894 | alpha and beta subunits | - |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
methylamine + H2O + 2 amicyanin = formaldehyde + NH3 + 2 reduced amicyanin | the rate-determining step in the reductive half-reaction of the bacterial enzyme methylamine dehydrogenase is the proton abstraction from the native substrate methylamine, ab initio QM/MM molecular dynamics simulations, average flow of electronic charge within the QM subsystem during proton transfer to OD1 computed from randomly selected subsets of the reactant, model comparisons, detailed overview | Paracoccus denitrificans |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
methylamine + H2O + 2 amicyanin | - |
Paracoccus denitrificans | formaldehyde + NH3 + 2 reduced amicyanin | - |
? |
Subunits | Comment | Organism |
---|---|---|
heterotetramer | - |
Paracoccus denitrificans |
Synonyms | Comment | Organism |
---|---|---|
MADH | - |
Paracoccus denitrificans |
methylamine dehydrogenase | - |
Paracoccus denitrificans |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
tryptophan tryptophylquinone | TTQ | Paracoccus denitrificans |
General Information | Comment | Organism |
---|---|---|
additional information | QM/MM molecular dynamics simulations at room temperature generate a multidimensional thermal free-energy landscape without restriction of the degrees of freedom beyond a multidimensional reaction subspace mapping two rather similar pathways for the underlying proton transfer to one of two aspartate carboxyl oxygen atoms, termed OD1 and OD2, which hydrogen bond with Thr122 and Trp108, respectively. Despite significant large-amplitude motion perpendicular to the one-dimensional proton transfer coordinate, due to fluctuations of the donor-acceptor distance of about 3 a, it is found that the one-dimensional proton transfer free-energy profiles are essentially identical to the minimum free-energy pathways on the multidimensional free-energy landscapes for both proton transfer channels. Proton transfer to one of the acceptor oxygen atoms (the OD2 site) is slightly favored in methylamine dehydrogenase both kinetically and thermodynamically. Modeling is based on the crysta structure of the substrate-free enzyme MADH from Paracoccus denitrificans resolved at 1.75 A, PDB ID 2BBK | Paracoccus denitrificans |