Controlled protonation of iron–molybdenum cofactor by nitrogenase: a structural and theoretical analysis

Abstract

Qualitative molecular modelling has been used to identify possible routes for transfer of protons from the surface of the nitrogenase protein to the iron–molybdenum cofactor (FeMoco) and to substrates during catalysis. Three proton-transfer routes have been identified; a water-filled channel running from the protein exterior to the homocitrate ligand of FeMoco, and two hydrogen-bonded chains to specific FeMoco sulphur atoms. It is suggested that the water channel is used for multiple proton deliveries to the substrate, as well as in diffusion of products and substrates between FeMoco and the bulk solvent, whereas the two hydrogen-bonded chains each allow a single proton to be added to, and subsequently depart from, FeMoco during the catalytic cycle. Possible functional differences in the proton-transfer channels are discussed in terms of assessment of the protein environment and specific hydrogen-bonding effects. The implications of these observations are discussed in terms of the suppression of wasteful production of dihydrogen by nitrogenase and the Lowe–Thorneley scheme for dinitrogen reduction.

Site-Directed Mutagenesis of the Anabaena sp. Strain PCC 7120 Nitrogenase Active Site To Increase Photobiological Hydrogen Production

“…In this regard, H195 of A. vinelandii nitrogenase, equivalent to the cyanobacterial H197, hydrogen bonds to the central bridging sulfur atom (S2B) between Fe2 and Fe6 of FeMo-co and was experimentally shown to be an obligate proton donor for nitrogenous substrates (N 2 , azide, and hydrazine), but not for reduction of acetylene (3,10,27). We speculate that His residues replacing Q193, R284, and F388 in the Anabaena enzyme could hydrogen bond to neighboring residues, a water molecule, or homocitrate (in the case of Q193H) and participate in the transfer of protons to H197 in the active site or to homocitrate, which is proposed to be part of a water-filled channel potentially involved in proton transfer (13). In this regard, the Q193S variant, which also exhibits similar high H 2 production rates under Ar or air, could similarly participate in proton transfer via a hydrogen-bonded chain.…”

“…Of interest, each of these highly active Anabaena variants is predicted to place an added His close to H197. The imidazole ring of the new residue could participate in His-mediated proton transfer to the FeMo-co site (13,22,51). In this regard, H195 of A. vinelandii nitrogenase, equivalent to the cyanobacterial H197, hydrogen bonds to the central bridging sulfur atom (S2B) between Fe2 and Fe6 of FeMo-co and was experimentally shown to be an obligate proton donor for nitrogenous substrates (N 2 , azide, and hydrazine), but not for reduction of acetylene (3,10,27).…”

Catalysis by Enzymes: The Biological Ammonia Synthesis

“…Numerous different binding sites for N 2 have been invested, and there is an ongoing argument on whether N 2 is bound and reduced on the Mo atom [84][85][86][87][88]94] or on the Fe atoms [27,55,[74][75][76][77][78]80,81,96,99,100,103]. As there are no experimental results on the structure of the FeMoco with coordinated N 2 H X species, this question is not definitely settled yet.…”

Symbiotic Nitrogen Fixation in Soybean

“…6). Therefore, the amount of these nutrients in the soil and plant uptake affects the symbiotic N 2 -fixation of legumes directly (Werner, 1987;Durrant, 2001). Fig.…”