Acta NaturaeActa NaturaeActa Naturae2075-8251Acta Naturae Ltd1075410.32607/20758251-2010-2-2-66-70ArticlesСтатьиResearch ArticleBioinformatic Analysis, Molecular Modeling of Role of Lys65 Residue in Catalytic Triad of D-aminopeptidase from Ochrobactrum anthropiBioinformatic Analysis, Molecular Modeling of Role of Lys65 Residue in Catalytic Triad of D-aminopeptidase from Ochrobactrum anthropiKhaliullinI G

Faculty of Bioengineering and Bioinformatics; Department of Chemistry

SuplatovD A

Faculty of Bioengineering and Bioinformatics

ShalaevaD N

Faculty of Bioengineering and Bioinformatics

OtsukaMAsanoYSvedasV K

Faculty of Bioengineering and Bioinformatics

vytas@belozersky.msu.ruLomonosov Moscow State UniversityBiotechnology Research Center, Toyama Prefectural University1506201022VOL 2, NO2 (2010)ТОМ 2, №2 (2010)667017012020Copyright ©; 2010, Khaliullin I.G., Suplatov D.A., Shalaeva D.N., Otsuka M., Asano Y., Svedas V.K.Copyright ©; 2010, Khaliullin I.G., Suplatov D.A., Shalaeva D.N., Otsuka M., Asano Y., Svedas V.K.2010Khaliullin I.G., Suplatov D.A., Shalaeva D.N., Otsuka M., Asano Y., Svedas V.K.Khaliullin I.G., Suplatov D.A., Shalaeva D.N., Otsuka M., Asano Y., Svedas V.K.https://creativecommons.org/licenses/by/4.0https://actanaturae.ru/2075-8251/article/view/10754

ABSTRACT A bioinformatic and phylogenetic study has been performed on a family of penicillin-binding proteins including D-aminopeptidases, D-amino acid amidases, DD-carboxypeptidases, and β-lactamases. Significant homology between D-aminopeptidase from Ochrobactrum anthropi and other members of the family has been shown and a number of conserved residues identified as S62, K65, Y153, N155, H287, and G289. Three of those (Ser62, Lys65, and Tyr153) form a catalytic triangle - the proton relay system that activates the generalized nucleophile in the course of catalysis. Molecular modeling has indicated the conserved residue Lys65 to have an unusually low pKa value, which has been confirmed experimentally by a study of the pH-profile of D-aminopeptidase catalytic activity. The resulting data have been used to elucidate the role of Lys65 in the catalytic mechanism of D-aminopeptidase as a general base for proton transfer from catalytic Ser62 to Tyr153, and vice versa, during the formation and hydrolysis of the acylenzyme intermediate.

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