Theoretical Analysis of the Dynamical Effects of the Amino Acid Residue Replacement in the Vicinity of the [4Fe–4S] Proximal Cluster on the O2-Tolerance of [NiFe]-Hydrogenases

Hydrogenases are enzymes that catalyze the reversible reaction, H2⇌2H++2e−, that occurs at the transition metal cluster in the catalytic center (e.g., [NiFe]). The catalytic activity of most standard hydrogenases is degraded by O2 under aerobic conditions (O2-sensitivity). However, the standard hydrogenase from Citrobacter sp. S-77 (termed S77 hereafter) can recover the activity; this phenomenon is called O2-tolerance. Contrarily, on the basis of the current classification of standard hydrogenases, the structural features of S77 appear to be O2-sensitive. The structural difference considered for the explanation seems to be just a replacement of an amino acid residue from Ser (most O2-sensitive standard hydrogenases) to Ala121 (S77). Nevertheless, this residue is spatially located far for the direct mechanical interaction with the relevant, functional metal cluster [4Fe–4S] (∼7 Å), which thus remains a mystery. In this study, we theoretically analyzed this problem and thereby provided an explanation regarding this experimental discrepancy.