The Hydrogen Chemistry of the FeMo-co Active Site of Nitrogenase
- 19 July 2005
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of the American Chemical Society
- Vol. 127 (31), 10925-10942
- https://doi.org/10.1021/ja0504946
Abstract
The chemical mechanism by which nitrogenase enzymes catalyze the hydrogenation of N2 (and other multiply bonded substrates) at the NcFe7MoS9(homocitrate) active site (FeMo-co) is unknown, despite the accumulation of much data on enzyme reactivity and the influences of key amino acids surrounding FeMo-co. The mutual influences of H2, substrates, and the inhibitor CO on reactivity are key experimental tests for postulated mechanisms. Fundamental to all aspects of mechanism is the accumulation of H atoms (from e- + H+) on FeMo-co, and the generation and influences of coordinated H2. Here, I argue that the first introduction of H is via a water chain terminating at water 679 (PDB structure 1M1N, Azotobactervinelandii) to one of the μ3-S atoms (S3B) of FeMo-co. Next, using validated density functional calculations of a full chemical representation of FeMo-co and its connected residues (α-275Cys, α-442His), I have characterized more than 80 possibilities for the coordination of up to three H atoms, and H2, and H + H2, on the S2A, Fe2, S2B, Fe6, S3B domain of FeMo-co, which is favored by recent targeted mutagenesis results. Included are calculated reaction profiles for movements of H atoms (between S and Fe, and between Fe and Fe), for the generation of Fe−H2, for association and dissociation of Fe−H2 at various reduction levels, and for H/H2 exchange. This is new hydrogen chemistry on an unprecedented coordination frame, with some similarities to established hydrogen coordination chemistry, and with unexpected and unprecedented structures such as Fe(S)3(H2)2(H) octahedral coordination. General principles for the hydrogen chemistry of FeMo-co include (1) the stereochemical mobility of H bound to μ3-S, (2) the differentiated endo- and exo- positions at Fe for coordination of H and/or H2, and (3) coordinative allosteric influences in which structural and dynamic aspects of coordination at one Fe atom are affected by coordination at another Fe atom, and by H on S atoms. Evidence of end-differentiation in FeMo-co is described, providing a rationale for the occurrence of Mo. The reactivity results are discussed in the context of the Thorneley−Lowe scheme for nitrogenase reactions, and especially the scheme for the HD reaction (2H+ + 2e- + D2 ⇒ 2HD), using a model containing an H-entry site and at least two coordinative sites on FeMo-co. I propose that S3B is the H-entry site, suggest details for the H+ shuttle to S3B and subsequent movement of H atoms around FeMo-co preparatory to the binding and hydrogenation of N2 and other substrates, and suggest how H could be transferred to an alkyne substrate. I propose that S2B (normally hydrogen bonded to α-195His) has a modulatory function and is not an H-entry site. Finally, the recent first experimental trapping of a hydrogenated intermediate with EPR and ENDOR characterization is discussed, leading to a consensual model for the intermediate.Keywords
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