Structural and functional insights into the flexible β-hairpin of glycerol dehydrogenase.

Taein Park, Huyen Nga Hoang, Jung Youn Kang, Jongseo Park, Sang A Mun, Minwoo Jin, Jihyeong Yang, Che-Hun Jung, Soo Hyun Eom

The FEBS journal 2023 Sep

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During glycerol metabolism, the initial step of glycerol oxidation is catalysed by glycerol dehydrogenase (GDH), which converts glycerol to dihydroxyacetone in a NAD+ -dependent manner via an ordered Bi-Bi kinetic mechanism. Structural studies conducted with GDH from various species have mainly elucidated structural details of the active site and ligand binding. However, the structure of the full GDH complex with both cofactor and substrate bound is not determined, and thus, the structural basis of the kinetic mechanism of GDH remains unclear. Here, we report the crystal structures of Escherichia coli GDH with a substrate analogue bound in the absence or presence of NAD+ . Structural analyses including molecular dynamics simulations revealed that GDH possesses a flexible β-hairpin, and that during the ordered progression of the kinetic mechanism, the flexibility of the β-hairpin is reduced after NAD+ binding. It was also observed that this alterable flexibility of the β-hairpin contributes to the cofactor binding and possibly to the catalytic efficiency of GDH. These findings suggest the importance of the flexible β-hairpin to GDH enzymatic activity and shed new light on the kinetic mechanism of GDH. © 2023 Federation of European Biochemical Societies.

Citation

Taein Park, Huyen Nga Hoang, Jung Youn Kang, Jongseo Park, Sang A Mun, Minwoo Jin, Jihyeong Yang, Che-Hun Jung, Soo Hyun Eom. Structural and functional insights into the flexible β-hairpin of glycerol dehydrogenase. The FEBS journal. 2023 Sep;290(17):4342-4355