8GOB

Crystal Structure of Glycerol Dehydrogenase in the presence of NAD+

8GOB の概要

• エントリーDOI: 10.2210/pdb8gob/pdb
• 分子名称: Glycerol dehydrogenase, ZINC ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (5 entities in total)
• 機能のキーワード: glycerol dehydrogenase, complex, oxidoreductase
• 由来する生物種: Escherichia coli K-12
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 81458.40

構造登録者

Park, T.,Hoang, H.N.,Kang, J.Y.,Park, J.,Mun, S.A.,Jin, M.,Yang, J.,Jung, C.-H.,Eom, S.H. (登録日: 2022-08-24, 公開日: 2023-06-14, 最終更新日: 2023-11-29)

主引用文献

Park, T.,Hoang, H.N.,Kang, J.Y.,Park, J.,Mun, S.A.,Jin, M.,Yang, J.,Jung, C.H.,Eom, S.H.
Structural and functional insights into the flexible beta-hairpin of glycerol dehydrogenase.
Febs J., 290:4342-4355, 2023

PubMed Abstract: 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.

PubMed: 37165682
DOI: 10.1111/febs.16813

実験手法

X-RAY DIFFRACTION (2.6 Å)