3D Structure Modeling of Alpha-Amino Acid Ester Hydrolase from Xanthomonas rubrilineans.
Alpha-amino acid ester hydrolase (EC 3.1.1.43, AEH) is a promising biocatalyst for the production of semi-synthetic β-lactam antibiotics, penicillins and cephalosporins. The AEH gene from Xanthomonas rubrilineans (XrAEH) was recently cloned in this laboratory. The three-dimensional structure of XrAEH was simulated using the homology modeling method for rational design experiments. The analysis of the active site was performed, and its structure was specified. The key amino acid residues in the active site - the catalytic triad (Ser175, His341 and Asp308), oxyanion hole (Tyr83 and Tyr176), and carboxylate cluster (carboxylate groups of Asp209, Glu310 and Asp311) - were identified. It was shown that the optimal configuration of residues in the active site occurs with a negative net charge -1 in the carboxylate cluster. Docking of different substrates in the AEH active site was carried out, which allowed us to obtain structures of XrAEH complexes with the ampicillin, amoxicillin, cephalexin, D-phenylglycine, and 4-hydroxy-D-phenylglycine methyl ester. Modeling of XrAEH enzyme complexes with various substrates was used to show the structures for whose synthesis this enzyme will show the highest efficiency.
Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Leninskie gory, 1/3, Moscow, Russian Federation, 119991 ; Innovations and High Technologies MSU Ltd, Tsimlyanskya Str., 16, office 96, Moscow, Russian Federation, 109559.
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Zarubina
Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Leninskie gory, 1/3, Moscow, Russian Federation, 119991.
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Uporov
Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Leninskie gory, 1/3, Moscow, Russian Federation, 119991 ; Innovations and High Technologies MSU Ltd, Tsimlyanskya Str., 16, office 96, Moscow, Russian Federation, 109559.
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Fedorchuk
Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Leninskie gory, 1/3, Moscow, Russian Federation, 119991 ; Innovations and High Technologies MSU Ltd, Tsimlyanskya Str., 16, office 96, Moscow, Russian Federation, 109559.
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Fedorchuk
State Research Institute for Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), 1-st Dorozhniy pr., 1, Moscow, Russian Federation, 117545.
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Sklyarenko
State Research Institute for Genetics and Selection of Industrial Microorganisms (GosNIIgenetika), 1-st Dorozhniy pr., 1, Moscow, Russian Federation, 117545.
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Yarotsky
Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Leninskie gory, 1/3, Moscow, Russian Federation, 119991 ; Innovations and High Technologies MSU Ltd, Tsimlyanskya Str., 16, office 96, Moscow, Russian Federation, 109559 ; A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskiy prospect, 33/2, Moscow, Russian Federation, 119071.
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Tishkov
Xanthomonas; alpha-amino acid ester hydrolase; computer simulation; docking; enzymatic synthesis of antibiotics; protein engineering; rubrilineans