5ZXL

Structure of GldA from E.coli

Summary for 5ZXL

• Entry DOI: 10.2210/pdb5zxl/pdb
• Descriptor: Glycerol dehydrogenase, ZINC ION, GLYCEROL, ... (6 entities in total)
• Functional Keywords: dehydrogenase, glycerol, catalytic, oxidoreductase
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 4
• Total formula weight: 156931.99

Authors

Zhang, J.,Lin, L. (deposition date: 2018-05-21, release date: 2019-03-20, Last modification date: 2023-11-22)

Primary citation

Zhang, J.,Nanjaraj Urs, A.N.,Lin, L.,Zhou, Y.,Hu, Y.,Hua, G.,Gao, Q.,Yuchi, Z.,Zhang, Y.
Structure of glycerol dehydrogenase (GldA) from Escherichia coli.
Acta Crystallogr F Struct Biol Commun, 75:176-183, 2019

PubMed Abstract: Escherichia coli (strain K-12, substrain MG1655) glycerol dehydrogenase (GldA) is required to catalyze the first step in fermentative glycerol metabolism. The protein was expressed and purified to homogeneity using a simple combination of heat-shock and chromatographic methods. The high yield of the protein (∼250 mg per litre of culture) allows large-scale production for potential industrial applications. Purified GldA exhibited a homogeneous tetrameric state (∼161 kDa) in solution and relatively high thermostability (T = 65.6°C). Sitting-drop sparse-matrix screens were used for protein crystallization. An optimized condition with ammonium sulfate (2 M) provided crystals suitable for diffraction, and a binary structure containing glycerol in the active site was solved at 2.8 Å resolution. Each GldA monomer consists of nine β-strands, thirteen α-helices, two 3-helices and several loops organized into two domains, the N- and C-terminal domains; the active site is located in a deep cleft between the two domains. The N-terminal domain contains a classic Rossmann fold for NAD binding. The O and O atoms of glycerol serve as ligands for the tetrahedrally coordinated Zn ion. The orientation of the glycerol within the active site is mainly stabilized by van der Waals and electrostatic interactions with the benzyl ring of Phe245. Computer modeling suggests that the glycerol molecule is sandwiched by the Zn and NAD ions. Based on this, the mechanism for the relaxed substrate specificity of this enzyme is also discussed.

PubMed: 30839292
DOI: 10.1107/S2053230X19000037

Experimental method

X-RAY DIFFRACTION (2.794 Å)