Glutamate Synthases are key enzymes in the early stages of the assimilation of ammonia in bacteria, yeast, and plants. Azospirillum brasilense glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive transfer of L-glutamine amide group to the (C2) carbon of 2-oxoglutarate(2OG) yielding two molecules of L-glutamate and whose function requires the transfer of ammonia and electrons among distinct catalytic sites. The NADPH-dependent Glutamate Synthase comprises of two subunits: alpha e beta. The α-subunit structure is composed of the following domains:
- Amidotransferase domain (1-422)
- Central domain (423-779)
- FMN binding domain (780-1203)
- C-terminal β-domain (1204-1432)
To obtain information on the mechanism of channel opening and ammonia tunneling, we undertook MD study of GltS in solution. Two 4 ns MD simulations of GltS in the substrate-free oxidized state and in the complex with its natural substrates L-glutamine and 2-oxoglutarate, reduced state. The results showed that in presence of the substrates the tunnel opens up to a radius of about 0.4 nm thus confirming the hypotheses path for the ammonia diffusion. It is interesting to note that in the substrate-free enzyme the tunnel opening is not observed. Furthermore, a cooperative domain closure motion upon the L-gln binding has been observed.
- M. Coiro, A. Di Nola, M. A. Vanoni, M. Aschi, A. Coda, D. Roccatano. Molecular dynamics simulation of interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates. Prot. Sci., 13, 2979-2991 (2004).