Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis

Mannose 2-epimerase (ME), a member of the acylglucosamine 2-epimerase (AGE) superfamily that catalyzes epimerization of D-mannose and D-glucose, has recently been characterized to have potential for D-mannose production. However, the substrate-recognition and catalytic mechanism of ME remains unknown. In this study, structures of Runella slithyformis ME (RsME) and its D254A mutant [RsME(D254A)] were determined in their apo forms and as intermediate-analog complexes [RsME–D-glucitol and RsME(D254A)–D-glucitol]. RsME possesses the (α/α)₆-barrel of the AGE superfamily members but has a unique pocket-covering long loop (loop_α7–α8). The RsME–D-glucitol structure showed that loop_α7–α8 moves towards D-glucitol and closes the active pocket. Trp251 and Asp254 in loop_α7–α8 are only conserved in MEs and interact with D-glucitol. Kinetic analyses of the mutants confirmed the importance of these residues for RsME activity. Moreover, the structures of RsME(D254A) and RsME(D254A)–D-glucitol revealed that Asp254 is vital for binding the ligand in a correct conformation and for active-pocket closure. Docking calculations and structural comparison with other 2-epimerases show that the longer loop_α7–α8 in RsME causes steric hindrance upon binding to disaccharides. A detailed substrate-recognition and catalytic mechanism for monosaccharide-specific epimerization in RsME has been proposed.