Experimental and computational studies on the unusual substrate specificity of branched-chain amino acid aminotransferase from Thermoproteus uzoniensis

• Published in: Archives of biochemistry and biophysics 2016-10, Vol.607, p.27-36
• Main Authors: Bezsudnova, Ekaterina Yu, Stekhanova, Tatiana N., Suplatov, Dmitry A., Mardanov, Andrey V., Ravin, Nikolai V., Popov, Vladimir O.
• Format: Article
• Language: English
• Subjects: Amino Acids, Branched-Chain - chemistry; Archaea; Binding Sites; Branched-chain amino acid aminotransferase; Computational Biology - methods; Computer Simulation; Crystallography, X-Ray; Glutamine - chemistry; Hydrogen-Ion Concentration; Kinetics; Models, Molecular; Molecular modeling; Protein Binding; Protein Conformation; Subfamily-specific positions; Substrate Specificity; Thermoproteus - enzymology; Transaminases - chemistry
• ISSN: 0003-9861; 1096-0384
• DOI: 10.1016/j.abb.2016.08.009

PLP-Dependent fold-type IV branched-chain amino acid aminotransferases (BCATs) from archaea have so far been poorly characterized. A new BCAT from the hyperthermophilic archaeon Thermoproteus uzoniensis (TUZN1299) has been studied. TUZN1299 was found to be highly active toward branched-chain amino acids (BCAAs), positively charged amino acids, l-methionine, l-threonine, l-homoserine, l-glutamine, as well as toward 2-oxobutyrate and keto analogs of BCAAs, whereas l-glutamate and α-ketoglutarate were not converted in the overall reaction. According to stopped-flow experiments, the enzyme showed the highest specificity to BCAAs and their keto analogs. In order to explain the molecular mechanism of the unusual specificity of TUZN1299, bioinformatic analysis was implemented to identify the subfamily-specific positions in the aminotransferase class IV superfamily of enzymes. The role of the selected residues in binding of various ligands in the active site was further studied using molecular modeling. The results indicate that Glu188 forms a novel binding site for positively charged and polar side-chains of amino acids. Lack of accommodation for α-ketoglutarate and l-glutamate is due to the unique orientation and chemical properties of residues 102–106 in the loop forming the A-pocket. The likely functional roles of TUZN1299 in cellular metabolism – in the synthesis and degradation of BCAAs – are discussed. [Display omitted] •Specificity of a new archaeal branched-chain amino acid aminotransferase is examined.•Unusually for BCATs the enzyme is active toward l-ornithine, l-arginine, l-lysine.•l-glutamate and α-ketoglutarate are not converted in the overall reaction.•Novel binding C-pocket for side chains of positively charged amino acids is revealed.•Lack of accommodation for α-ketoglutarate is due to properties of residues 102–106.