Steviol glycosides (SGs) from Stevia rebaudiana Bertoni is a widely used sweetener with the advantage of high sweet and low in calories. Stevioside (ST) and Rebaudioside A (Reb A) with a bitter aftertaste are the main sweetening components in SGs. Reb M is a highly potency sweetener with almost no bitter aftertaste but is found in low content in S. rebaudiana Bertoni. In this study, the pre- and post-catalytic differences of stevioside glycosyltransferase SrUGT76G1 were investigated through long-time molecular dynamics simulations. SrUGT76G1 was mutated to enhance its efficiency in catalyzing the synthesis of Reb D to Reb M by identifying the enzyme mutation site through an integrated three-in-one approach that combines hinge region analysis, coevolutionary conservation, and energy calculations. The kcat and kcat/Km values of the M88V mutant with Reb D as substrate were 2.18-fold and 4.85-fold higher than those of wild-type SrUGT76G1, respectively. In addition, the M88V mutant coupled with sucrose synthase StSUS1 increased the yield of Reb M synthesis from Reb D to 92.40%. The present study provides an effective method for rapid search for mutation sites in the enzyme and for increasing the yield of Reb M.
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