How Can Methanol Dehydrogenase from Methylacidiphilum fumariolicum Work with the Alien Ce^III Ion in the Active Center? A Theoretical Study

Abstract

Lanthanides are an example of nonbiogenic metal species and have been widely used in crystallographic and spectroscopic studies to probe Mg /Ca binding sites in metalloproteins by replacing the native cofactor. Recently, a methanol dehydrogenase (MDH) enzyme containing cerium ion in the active site has been isolated from Methylacidiphilum fumariolicum bacterium. With the aim to highlight as metal ion substitution can be reflected in catalytic mechanism, a comparative DFT study between Ca- and Ce-MDH has been undertaken. The obtained potential energy surfaces (PES), for two considered reaction mechanisms (named A and B), indicate mechanism A (addition-elimination and protonation processes) as the favored for both the enzymes and show as the barrier for the rate-determining step of Ce-MDH requires 19.4 kcal mol .

Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide‐Dependent Methanol Dehydrogenase Activity

“…The former is unlikely based on consideration of the Lewis acidity of the coordinating metal ions. Therefore, we propose that a chemical rationale for XoxG′s diminished E m , by 80 mV, relative to that of MxaG, is that the stronger Lewis acidity of the Ln III cofactor makes methanol oxidation more favorable in the Ln‐MDH than in the Ca‐MDH, and therefore requires a lesser driving force to be provided by electron extraction from the metal‐bound PQQ cofactor by the cytochrome c L . Based on our crystallographic characterization of XoxG viewed in the context of MxaG and other cytochromes c , the structural rationale for this lower potential might be linked to greater solvent accessibility of the heme pocket in XoxG (Figures and S7).…”

Essential and Ubiquitous: The Emergence of Lanthanide Metallobiochemistry

“…It should be noted that this and other DFT studies included protonated PQQ carboxylate moieties;t he protonation state of those groups may influence the donor abilities of PQQ and whether these are partially deprotonated in the enzyme remains elusive in the crystal structures. [23b, 36,37] Previous work with Ca-MDH implicated two possible reaction mechanisms for the dehydrogenation of methanol ( Figure 5). In the addition-elimination mechanism, substrate adds directly to the PQQ carbonyl to form ah emi-ketalate intermediate.W hereas,i n the hydride transfer mechanism, there is direct transfer of ah ydride equivalent to PQQ.T hese two mechanisms were proposed partially based upon i) crystallographic studies, [38] ii)studies of biomimetic complexes [39] and iii)theoretical modelling of the reaction pathways.…”

“…In the addition-elimination mechanism, substrate adds directly to the PQQ carbonyl to form ah emi-ketalate intermediate.W hereas,i n the hydride transfer mechanism, there is direct transfer of ah ydride equivalent to PQQ.T hese two mechanisms were proposed partially based upon i) crystallographic studies, [38] ii)studies of biomimetic complexes [39] and iii)theoretical modelling of the reaction pathways. [37,40] In terms of mechanistic studies of the Ln-MDH enzyme active site,M arino et al investigated the mechanism of methanol oxidation in the presence of Ce 3+ using DFT.T hey claimed that the formation of the nucleophile (methanolate) and an intermediate (hemiketal) were thermodynamically stabilized in Ce-MDH compared to Ca-MDH. [37b] With the spectroscopically interesting lanthanides in the active sites of these enzymes,itisexpected that also experimentally progress will be made on elucidating the mechanism further.…”

The Catalytic Mechanism of Human Transketolase

“…Atom O4 is involved in hydrogen bonds with residues Asp424B, His37A and His109 A, while atom O3 is involved in a hydrogen bond with His258A. [40][41][42][43][44] The final models consisted of 184 and 188 atoms (X5P and E4P-dependent reactions, respectively; see Scheme S1), and had a total charge of + 1. Moreover, water molecule w1 establishes hydrogen bonds with atom O1 (atom numbering in Figure 1) and with another water molecule w2, both present in the system.…”

“…The residues have been modelled according to standard cluster model procedures. [40][41][42][43][44] The final models consisted of 184 and 188 atoms (X5P and E4P-dependent reactions, respectively; see Scheme S1), and had a total charge of + 1.…”