Cross-Talk and Ammonia Channeling between Active Centers in the Unexpected Domain Arrangement of Glutamate Synthase

Abstract

Introduction: The complex iron-sulfur flavoprotein glutamate synthase catalyses the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine, a reaction in the plant and bacterial pathway for ammonia assimilation. The enzyme functions through three distinct active centers carrying out L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor. Results: The 3.0 Å crystal structure of the dimeric 324 kDa core protein of a bacterial glutamate synthase was solved by the MAD method, using the very weak anomalous signal of the two 3Fe-4S clusters present in the asymmetric unit. The 1472 amino acids of the monomer fold into a four-domain architecture. The two catalytic domains have canonical Ntn-amidotransferase and FMN binding (β/α) 8 barrel folds, respectively. The other two domains have an unusual “cut (β/α) 8 barrel” topology and an unexpected novel β-helix structure. Channeling of the ammonia intermediate is brought about by an internal tunnel of 31 Å length, which runs from the site of L-glutamine hydrolysis to the site of L-glutamate synthesis. Conclusions: The outstanding property of glutamate synthase is the ability to coordinate the activity of its various functional sites to avoid wasteful consumption of L-glutamine. The structure reveals two polypeptide segments that connect the catalytic centers and embed the ammonia tunnel, thus being ideally suited to function in interdomain signaling. Depending on the enzyme redox and ligation states, these signal-transducing elements may affect the active site geometry and control ammonia diffusion through a gating mechanism.