[Fe]-hydrogenase functions in the methanogenic pathway of hydrogenotrophic methanogenic archaea. It catalyzes thereversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT and a proton by transferring a hydride ion to the proR position of the C14a carbon atom of methylene-H4MPT. This third type of hydrogenase contains a unique iron–guanylylpyridinol (FeGP) cofactor, in which the iron atom is ligated by one cysteine sulfur atom, two CO groups, one solvent molecule, and an sp2-hybridized nitrogen atom and an acyl carbon atom from the pyridinol ring. Three globular folding units of this protein form two clefts that serve as substrate-binding and active sites and that can be open or closed. Structural data are presented for the apoenzyme in a closed form, the holoenzyme (enzyme with the FeGP cofactor), the C176A holoenzyme, and the binary C176A holoenzyme-methylene-H4MPT complex in an open form. A closed and potentially active binary complex has been reliably modeled on the basis of the open binary complex and the closed apoenzyme. In this model, the iron center sits near the Re face of the imidazolidine ring of the substrate. The iron ligation site trans to the acyl carbon atom is next to the C14a carbon atom and is therefore considered to be the H2 binding site.