3D Structure Modeling of Alpha-Amino Acid Ester Hydrolase from Xanthomonas rubrilineans

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  • Authors: Zarubina S.A.1,2, Uporov I.V.1, Fedorchuk E.A.1,2, Fedorchuk V.V.1,2, Sklyarenko A.V.3, Yarotsky S.V.3, Tishkov V.I.1,2,4
  • Affiliations:
    1. Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University
    2. Innovations and High Technologies MSU Ltd
    3. State Research Institute for Genetics and Selection of Industrial Microorganisms (GosNIIgenetika)
    4. A.N. Bach Institute of Biochemistry, Russian Academy of Sciences
  • Issue: Vol 5, No 4 (2013)
  • Pages: 62-70
  • Section: Research Articles
  • URL: http://actanaturae.ru/2075-8251/article/view/10572
  • DOI: https://doi.org/10.32607/20758251-2013-5-4-62-70
  • Cite item

Abstract


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.


3D Structure Modeling of Alpha-Amino Acid Ester Hydrolase from Xanthomonas rubrilineans

S. A. Zarubina

Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Innovations and High Technologies MSU Ltd

Author for correspondence.
Email: vitishkov@gmail.com

Russian Federation

I. V. Uporov

Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University

Email: vitishkov@gmail.com

Russian Federation

E. A. Fedorchuk

Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Innovations and High Technologies MSU Ltd

Email: vitishkov@gmail.com

Russian Federation

V. V. Fedorchuk

Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Innovations and High Technologies MSU Ltd

Email: vitishkov@gmail.com

Russian Federation

A. V. Sklyarenko

State Research Institute for Genetics and Selection of Industrial Microorganisms (GosNIIgenetika)

Email: vitishkov@gmail.com

Russian Federation

S. V. Yarotsky

State Research Institute for Genetics and Selection of Industrial Microorganisms (GosNIIgenetika)

Email: vitishkov@gmail.com

Russian Federation

V. I. Tishkov

Department of Chemical Enzymology, Faculty of Chemistry, M.V. Lomonosov Moscow State University; Innovations and High Technologies MSU Ltd; A.N. Bach Institute of Biochemistry, Russian Academy of Sciences

Email: vitishkov@gmail.com

Russian Federation

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Copyright (c) 2013 Zarubina S.A., Uporov I.V., Fedorchuk E.A., Fedorchuk V.V., Sklyarenko A.V., Yarotsky S.V., Tishkov V.I.

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