Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation

Abstract

The catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (MDH) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (PQQ). A crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. A theoretical analysis and an improved refinement of the 1.9-Å resolution crystal structure of MDH from Methylophilus methylotrophus W3A1 in the presence of methanol, reported earlier, indicates that the observed tetrahedral configuration of the C-5 atom of PQQ in that study represents the C-5-reduced form of the cofactor and lends support for a hydride transfer mechanism for MDH. Methanol and glucose dehydrogenases are two well studied quinoproteins that use 2,7,9-tricarboxypyrroloquinoline quinone (PQQ) as a cofactor ( Fig. 1A; refs. 1-4). Both enzymes require a divalent cation such as Ca 2ϩ for catalytic activity. Crystallographic studies have been reported for both methanol dehydrogenase (MDH) and glucose dehydrogenase (5-12). These crystallographic investigations have not only provided detailed information concerning the PQQ binding site, but they have also established structural frameworks for mechanistic elucidation. Two plausible mechanisms have been proposed. The first one (Fig. 1B) involves a nucleophilic addition of the alcohol to the C-5 carbonyl followed by an intramolecular retro-ene reaction (13-16). The second mechanism (Fig. 1C) involves a general base initiated hydride transfer from the alcohol to the C-5 carbonyl carbon and subsequent tautomerization of the hydride transfer intermediate to the reduced PQQH2 (15-17). Accurate structural information will be valuable in distinguishing these two proposed mechanisms.Recently, a high-resolution structure of methanol dehydrogenase from Methylophilus methylotrophus W3A1 in a second crystal form has been reported (8). Surprisingly, even when planarity constraints were applied during the structural refinement, the refined structure displayed a C-5 center significantly distorted from planarity. Although the cofactor was assigned to be the semiquinone form of PQQ, this did not provide a satisfactory explanation as to why the C-5 center is tetrahedral, because earlier quantum mechanical studies had demonstrated that the tricyclic ring in the semiquinone form of PQQ is essentially planar in the presence or absence of Ca 2ϩ (17). The C-5 methanol adduct could give a tetrahedral C-5 center, but it is not compatible with the electron density map. The tautomeric form of the reduced PQQ, in which the pyrrole H-N hydrogen is moved to the C-5 carbon, does not seem to be plausible owning to a strong intramolecular hydrogen bond interaction between the pyrrole H-N and one of the C-9 carboxylate oxygen atoms. Thus, the observed tetrahedral C-5 remained an unresolved issue. However, if one loo...

Structure of the Pyrroloquinoline Quinone Radical in Quinoprotein Ethanol Dehydrogenase

“…1), the role of which as a potential vitamin in mammals is currently under debate (4 -6). Among this class of enzymes, methanol dehydrogenase (MDH) (7)(8)(9)(10)(11)(12)(13)(14)(15), quinoprotein ethanol dehydrogenase (QEDH) (16), quinohemoprotein alcohol dehydrogenase (QH-ADH) (17,18), and soluble glucose dehydrogenase (s-GDH) (19) have been described and crystallized. Spectroscopic, biochemical, and in particular x-ray crystallographic studies have allowed great progress to be made in the understanding of the structure and function of these proteins (20 -22).…”

Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase

“…Attempts to crystallize MDH with MeOH substrate at the active site have not yet been successful (10,12,13). The hydride transfer mechanism was shown to be correct by x-ray crystallography (10).…”

“…10) of the reduced PQQ bound to MDH presents Wat1 hydrogen bonding to the -CO 2 Ϫ group of Asp-297 (Asp-297-CO 2 Ϫ ) and ϪCO 2 Ϫ group of Glu-171 (Glu-171-CO 2 Ϫ ) associated with Ca 2ϩ . Attempts to crystallize MDH with MeOH substrate at the active site have not yet been successful (10,12,13). The hydride transfer mechanism was shown to be correct by x-ray crystallography (10).…”

“…1-4). More recently, our attention has been directed to the employment of computational methods, particularly in the mechanism of the oxidation of methanol and glucose by the appropriate quinoprotein enzymes (5)(6)(7)(8)(9)(10)(11).…”

Mechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: A computational approach

“…From the x-ray structure (Protein Data Bank ID code 1G72) of the enzyme-bound intermediate (12), the MDH⅐PQQ is modeled so that the C5 of PQQ is a planar, rather than a tetrahedral, configuration of the crystal structure. Subsequently, methanol was docked into the active site of that complex (13) )⅐methanol structures, respectively.…”