Download MendeleyStructure of glycerol dehydrogenase (GldA) from Escherichia coli.
Zhang, J., Nanjaraj Urs, A.N., Lin, L., Zhou, Y., Hu, Y., Hua, G., Gao, Q., Yuchi, Z., Zhang, Y.(2019) Acta Crystallogr F Struct Biol Commun 75: 176-183
- PubMed: 30839292
- DOI: https://doi.org/10.1107/S2053230X19000037
- Primary Citation of Related Structures:
5ZXL - 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 m = 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 10 -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 1 and O 2 atoms of glycerol serve as ligands for the tetrahedrally coordinated Zn 2+ 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 2+ and NAD + ions. Based on this, the mechanism for the relaxed substrate specificity of this enzyme is also discussed.
Organizational Affiliation:
The Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China.
