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Crystal Structure of Glycerol Dehydrogenase from Klebsiella pneumoniae

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Glycerol dehydrogenase (GlyDH) plays a crucial role in the glycerol metabolism pathway by catalyzing the oxidation of glycerol to dihydroxyacetone (DHA). Previous studies of GlyDH have predominantly focused on unraveling the structural features of the active site and its binding interactions with ligand. However, the structural details of GlyDH in complex with both NAD+ and the substrate bound have remained elusive. In this study, we present the crystal structures of Klebsiella pneumoniae GlyDH (KpGlyDH) in the absence and presence of NAD+ at a resolution of 2.1 Å. Notably, both structures reveal the binding of the substrate, ethylene glycol, to the zinc ion. Interestingly, a significant change in the coordination number of the zinc ion is observed, with three in the absence of NAD+ and four in its presence. These findings shed light on the structural aspects of GlyDH and its interactions with NAD+ and the substrate.

Abstract

Glycerol dehydrogenase (GlyDH) plays a crucial role in the glycerol metabolism pathway by catalyzing the oxidation of glycerol to dihydroxyacetone (DHA). Previous studies of GlyDH have predominantly focused on unraveling the structural features of the active site and its binding interactions with ligand. However, the structural details of GlyDH in complex with both NAD+ and the substrate bound have remained elusive. In this study, we present the crystal structures of Klebsiella pneumoniae GlyDH (KpGlyDH) in the absence and presence of NAD+ at a resolution of 2.1 Å. Notably, both structures reveal the binding of the substrate, ethylene glycol, to the zinc ion. Interestingly, a significant change in the coordination number of the zinc ion is observed, with three in the absence of NAD+ and four in its presence. These findings shed light on the structural aspects of GlyDH and its interactions with NAD+ and the substrate.

참고문헌 (39)

  1. Spencer, P., "Isolation and characterisation of the glycerol dehydrogenase from Bacillus stearothermophilus", Biochim Biophys Acta, 994, pp.270~ (1989)
  2. Scharschmidt, M., "Isolierung und Charakterisierung von Glycerin-Dehydrogenase ausBacillus megaterium", Hoppe-Seyler’s Zeitschrift Für Physiologische Chemie, 364, pp.911~ (1983)
  3. Viswanath-Reddy, M., "Purification and Properties of NADP+-linked Glycerol Dehydrogenase from Neurospora crassa", Journal of General Microbiology, 107, pp.289~ (1978)
  4. May, J. W., "Glycerol Utilization by Schizosaccharomyces pombe: Dehydrogenation as the Initial Step", Microbiology, 123, pp.183~ (1981)
  5. Kormann, A. W., "Purification and properties of an NADP + -dependent glycerol dehydrogenase from rabbit skeletal muscle", Biochim Biophys Acta, 258, pp.40~ (1972)
  6. Wichmann, R., "Cofactor regeneration at the lab scale", Adv Biochem Eng Biotechnol, 92, pp.225~ (2005)
  7. Leichus, B. N., "Isotopic analysis of the reaction catalyzed by glycerol dehydrogenase", Biochemistry, 33, pp.14642~ (1994)
  8. Tang, C. T., "Purification and properties of a nicotinamide adenine dinucleotide-linked dehydrogenase that serves an Escherichia coli mutant for glycerol catabolism", J Bacteriol, 140, pp.182~ (1979)
  9. Beauchamp, J, "Characterization of Thermotoga maritima glycerol dehydrogenase for the enzymatic production of dihydroxyacetone", Appl Microbiol Biotechnol, 98, pp.7039~ (2014)
  10. Hekmat, D., "Optimization of the microbial synthesis of dihydroxyacetone from glycerol with Gluconobacter oxydans", Bioprocess Biosyst Eng, 26, pp.109~ (2003)
  11. Weckbecker, A., "Regeneration of nicotinamide coenzymes: principles and applications for the synthesis of chiral compounds", Adv Biochem Eng Biotechnol, 120, pp.195~ (2010)
  12. Tao, F., "Genome sequence of Klebsiella pneumoniae LZ, a potential platform strain for 1,3-propanediol production", J Bacteriol, 194, pp.4457~ (2012)
  13. Petrov, K., "High production of 2,3-butanediol from glycerol by Klebsiella pneumoniae G31", Appl Microbiol Biotechnol, 84, pp.659~ (2009)
  14. Oh, B. R., "Efficient production of ethanol from crude glycerol by a Klebsiella pneumoniae mutant strain", Bioresour Technol, 102, pp.3918~ (2011)
  15. Liu, H., "1,3-Propanediol and its copolymers: research, development and industrialization", Biotechnol J, 5, pp.1137~ (2010)
  16. Yang, F, "Value-added uses for crude glycerol--a byproduct of biodiesel production", Biotechnol Biofuels, 5, pp.13~ (2012)
  17. Saxena, R. K., "Microbial production of 1,3-propanediol:Recent developments and emerging opportunities", Biotechnol Adv, 27, pp.895~ (2009)
  18. Zhang, H., "Engineering of glycerol dehydrogenase for improved activity towards 1, 3-butanediol", Appl Microbiol Biotechnol, 88, pp.117~ (2010)
  19. Raynaud, C., "Molecular characterization of the glyceroloxidative pathway of Clostridium butyricum VPI 1718", J Bacteriol, 193, pp.3127~ (2011)
  20. Tang, J. C., "Immunochemical properties of NAD+-linked glycerol dehydrogenases from Escherichia coli and Klebsiella pneumoniae", J Bacteriol, 152, pp.1169~ (1982)
  21. Wang, Y., "Glycerol dehydrogenase plays a dual role in glycerol metabolism and 2,3-butanediol formation in Klebsiella pneumoniae", J Biol Chem, 289, pp.6080~ (2014)
  22. Ko, G. S., "Biochemical and Molecular Characterization of Glycerol Dehydrogenas from Klebsiella pneumoniae", J Microbiol Biotechnol, 30, pp.271~ (2020)
  23. Park, T., "Structural and functional insights into the flexible beta-hairpin of glycerol dehydrogenase", FEBS J, 290, pp.4342~ (2023)
  24. Chauliac, D., "Kinetic characterization and structure analysis of an altered polyol dehydrogenase with d-lactate dehydrogenase activity", Protein Sci, 29, pp.2387~ (2020)
  25. Zhang, J., "Structure of glycerol dehydrogenase (GldA) from Escherichia coli", Acta Crystallogr F Struct Biol Commun, 75, pp.176~ (2019)
  26. Hatti, K., "Seeing but not believing: the structure of glycerol dehydrogenase initially assumed to be the structure of a survival protein from Salmonella typhimurium", Acta Crystallogr D Struct Biol, 73, pp.609~ (2017)
  27. Musille, P, "Structure of glycerol dehydrogenase from Serratia", Acta Crystallogr F Struct Biol Commun, 70, pp.166~ (2014)
  28. Lesley, S. A., "Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline", Proc Natl Acad Sci U.S.A, 99, pp.11664~ (2002)
  29. Ruzheinikov, S. N., "Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase", Structure, 9, pp.789~ (2001)
  30. Hoang, H. N., "The Activation of Glycerol Dehydrogenase from Escherichia coli by ppGpp", Bulletin of the Korean Chemical Society, 41, pp.133~ (2020)
  31. Gartner, G., "Purification and Properties of Glycerol Dehydrogenase from Candida valida", Microbiology, 130, pp.3225~ (1984)
  32. Minor, W., "HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes", Acta Crystallogr D Biol Crystallogr, 62, pp.859~ (2006)
  33. Winn, M. D., "Overview of the CCP4 suite and current developments", Acta Crystallogr D Biol Crystallogr, 67, pp.235~ (2011)
  34. Emsley, P., "Features and development of Coot", Acta Crystallogr D Biol Crystallogr, 66, pp.486~ (2010)
  35. Adams, P. D., "PHENIX: a comprehensive Python-based system for macromolecular structure solution", Acta Crys tallogr D Biol Crystallogr, 66, pp.213~ (2010)
  36. Dokmanic, I., "Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination", Acta Crystallogr D Biol Crystallogr, 64, pp.257~ (2008)
  37. Krissinel, E., "Inference of macromolecular assemblies from crystalline state", J Mol Biol, 372, pp.774~ (2007)
  38. Pavelka, A., "CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules", IEEE, 2016, pp.13, 505~
  39. Chovancova, E., "CAVER 3.0:a tool for the analysis of transport pathways in dynamic protein structures", PLoS Comput Biol, 8, pp.e1002708~ (2012)

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