8GOA

Crystal Structure of Glycerol Dehydrogenase in the absence of NAD+

Summary for 8GOA

• Entry DOI: 10.2210/pdb8goa/pdb
• Descriptor: Glycerol dehydrogenase, ZINC ION, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total)
• Functional Keywords: glycerol dehydrogenase, complex, oxidoreductase
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 4
• Total formula weight: 160995.96

Authors

Park, T.,Hoang, H.N.,Kang, J.Y.,Park, J.,Mun, S.A.,Jin, M.,Yang, J.,Jung, C.-H.,Eom, S.H. (deposition date: 2022-08-24, release date: 2023-06-14, Last modification date: 2023-09-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.9 Å)