additional information |
the 3D dimeric structure of BADH2 is modeled using homology modeling. Each monomer comprises of 3 domains (substrate-binding, NAD+-binding, and oligomerization domains). The NAD+-binding domain is the most mobile. A scissor-like motion is observed between the monomers. Inside the binding pocket, N162 and E260 are tethered by strong hydrogen bonds to residues in close proximity. In contrast, the catalytic C294 is very mobile and interacts occasionally with N162. The flexibility of the nucleophilic C294 can facilitate the attack of free carbonyl on an aldehyde substrate. Mainly, N162, E260, C294 are found to play a role in catalytic activity. C294 and E260 are involved in a key step of hemithioacetal-enzyme formation, while N162 helps stabilize an intermediate. Molecular dynamics (MD) simulations of substrate-bound enzyme. Both N162 and C294 form different degrees of hydrogen bonds. C294 seems to weakly hydrogen bond with adjacent amino acids (below 1% of hydrogen bonds with N162), whereas N162 forms a strong hydrogen bond with Q292 (over90%). Apparently, C294 seems to be flexible, whilst N162 is tethered by Q292 inside a pocket. The catalytic C294 is located in the middle of a cavity. The high flexibility of C294 which supports the role of the nucleophile C294's ability to attack a free carbonyl group of a bound substrate. On the contrary, N162 and E260 appear to be rigid due to strong interactions with their neighbours. Such interactions tethering N162 and E260 may help to shape a suitable environment for a catalytic activity |
Oryza sativa Japonica Group |