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Objective To understand the molecular basis for a potential reaction mechanism and develop novel antibiotics with homology modeling for 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase (HMGS). Methods The genetic engineering technology and the composer module of SYBYL7.0 program were used,while the HMGS three-dimensional structure was analyzed by homology modeling. Results The mvaS gene was cloned from Streptococcus pneumoniae and overexpressed in Escherichia coli from a pET28 vector.The expressed enzyme (about 46 kDa) was purified by affinity chromatography with a specific activity of 3.24 μmol/min/mg.Optimal conditions were pH 9.75 and 10 mmol/L MgCl2 at 37℃.The Vmax and Km were 4.69 μmol/mirdmg and 213 μmol/L respectively.The 3D model of S.pneumoniae HMGS was established based on structure template of HMGS of Enterococcus faecalis. Conclusion The structure of HMGS will facilitate the structure-based design of alternative drugs to cholesterol-lowering therapies or to novel antibiotics to the Gram-positive cocci,whereas the recombinant HMGS will prove useful for drug development against a different enzyme in the mevalonate pathway.