Protein of Unknown Function from Bacterium Variovorax paradoxus with the Amino Acid Substitution N174k Capable of Forming Schiff Base with a PLP Molecule

Abstract

Pyridoxal 5'-phosphate (PLP)-dependent enzymes are among the most abundant enzymes present in nearly all organisms, where they perform more than 150 different catalytic functions. Based on the three-dimensional structures, these enzymes are classified into seven (I–VII) different fold types. In these enzymes, the cofactor is bound as a Schiff base with the conserved active-site lysine residue. Recently, we have discovered the protein from the bacterium Variovorax paradoxus (VAPA), which belongs to the fold type IV and has a significant structural similarity to transaminases. It contains an asparagine residue at the position of catalytic lysine in fold type IV transaminases and, consequently, it cannot form a Schiff base with PLP and does not have aminotransferase activity. In this study, a single-point mutant of the VAPA protein with the N174K substitution was obtained and its three-dimensional structure was determined. An analysis of the obtained data showed that the introduced mutation restores the ability of  VAPA to form a Schiff base with the cofactor.