Structural Basis of the Hydride Transfer Mechanism in F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase

Abstract

F₄₂₀-dependent methylenetetrahydromethanopterin (methylene-H₄MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H₄MPT⁺ and methylene-H₄MPT using coenzyme F₄₂₀ as hydride carrier. We determined the structures of the Mtd−methylene-H₄MPT, Mtd−methenyl-H₄MPT⁺, and the Mtd−methenyl-H₄MPT⁺-F₄₂₀H₂ complexes at 2.1, 2.0, and 1.8 Å resolution, respectively. The pterin−imidazolidine−phenyl ring system is present in a new extended but not planar conformation which is virtually identical in methenyl-H₄MPT⁺ and methylene-H₄MPT at the current resolution. Both substrates methenyl-H₄MPT⁺ and F₄₂₀H₂ bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms, respectively. The polypeptide scaffold does not reveal any significant conformational change upon binding of the bulky substrates but in turn changes the conformations of the substrate rings either to avoid clashes between certain ring atoms or to adjust the rings involved in hydride transfer for providing an optimal catalytic efficiency.