Cytidine deaminases catalyze the conversion of <i>N</i> ( <i>S</i> , <i>O</i> ) ⁴ -substituted pyrimidine nucleosides

Abstract

Cytidine deaminases (CDAs) catalyze the hydrolytic deamination of cytidine and 2'-deoxycytidine to uridine and 2'-deoxyuridine. Here, we report that prokaryotic homo-tetrameric CDAs catalyze the nucleophilic substitution at the fourth position of <i>N</i>⁴-acyl-cytidines, <i>N</i>⁴-alkyl-cytidines, and <i>N</i>⁴-alkyloxycarbonyl-cytidines, and <i>S</i>⁴-alkylthio-uridines and <i>O</i>⁴-alkyl-uridines, converting them to uridine and corresponding amide, amine, carbamate, thiol, or alcohol as leaving groups. The x-ray structure of a metagenomic CDA_F14 and the molecular modeling of the CDAs used in this study show a relationship between the bulkiness of a leaving group and the volume of the binding pocket, which is partly determined by the flexible β3α3 loop of CDAs. We propose that CDAs that are active toward a wide range of substrates participate in salvage and/or catabolism of variously modified pyrimidine nucleosides. This identified promiscuity of CDAs expands the knowledge about the cellular turnover of cytidine derivatives, including the pharmacokinetics of pyrimidine-based prodrugs.