The atomic-resolution crystal structure of activated [Fe]-hydrogenase

Abstract

Hydrogenases are promising templates for constructing new H2-based catalysts. [Fe]-hydrogenase, which features an iron-guanylylpyridinol (FeGP) cofactor, catalyses a reversible hydride transfer from H2 to methenyl-tetrahydromethanopterin (methenyl-H4MPT+, a C1 carrier in methanogens). Here, we present a detailed mechanistic scenario of this reaction based on the 1.06 A resolution structure of [Fe]-hydrogenase in a closed active form, in which the Fe of the FeGP cofactor is positioned near the hydride-accepting C14a of a remarkably distorted methenyl-H4MPT+. The open-to-closed transition generates an unsaturated pentacoordinated Fe on expulsion of a water ligand. Quantum mechanics/molecular mechanics computations based on experimental models indicate that a deprotonated 2-OH group on the FeGP cofactor acts as a catalytic base and provides a fairly complete picture of H2 activation: H2 binding on the empty Fe site was found to be nearly thermo-neutral while H2 cleavage and hydride transfer proceed smoothly. The overall reaction involves a repositioning and relaxation of the distorted methenyl-H4MPT+. Detailed knowledge about its catalytic process is important for exploiting [Fe]-hydrogenase—an enzyme that cleaves and produces H2—for technological purposes. This study presents an atomic-resolution crystal structure of a substrate-bound closed active form of the enzyme and a precise catalytic cycle.