Improved nucleoside (2'-deoxy)ribosyltransferases maximize enzyme promiscuity while maintaining catalytic efficiency

Nucleoside analogues have been extensively used to treat viral and bacterial infections and cancer for more than 60 years. However, their chemical synthesis is complex and often requires multiple steps and a dedicated synthetic route for every new nucleoside to be produced. Wild type nucleoside 2′-deoxyribosyltransferase enzymes are promising for biocatalysis. Guided by the structure of the enzyme from the thermophilic organism Chroococcidiopsis thermalis PCC 7203 (CtNDT) bound to the ribonucleoside analogue Immucillin-H, we designed mutants of CtNDT and the psychrotolerant Bacillus psychrosaccharolyticus (BpNDT) to improve catalytic efficiency with 3′-deoxynucleosides and ribonucleosides, while maintaining nucleobase promiscuity to generate over 100 distinct nucleoside products. Enhanced catalytic efficiency toward ribonucleosides and 3′-deoxyribonucleosides occurred via gains in turnover rate, rather than improved substrate binding. We determined the crystal structures of two engineered variants as well as kinetic parameters with different substrates, unveiling molecular details underlying their expanded substrate scope. Our rational approach generated robust enzymes and a roadmap for reaction conditions applicable to a wide variety of substrates.