Comment on binding affinity determines substrate specificity and enables discovery of substrates for N-Myristoyltransferases

Overview & Synopsis

Establishing the protein posttranslational modification (PTM) landscape at the proteome scale relies on the target specificity of the relevant enzyme catalysts. Su et al. (ACS Catal, 2021:14877) proposed that “the kcat/Km value is not the best parameter to determine the in vivo substrate specificity of an enzyme. Instead, the binding affinities of substrates are more important for determining the substrate specificity of enzymes in a physiological setting”. The authors extended their conclusions to any “substrate pairs for enzymes that catalyze PTM”. This study provides a springboard for the discussion of the relative merits of different approaches used to identify protein modification targets. My point of view is that the specificity constant kcat/Km remains a highly relevant parameter for defining specificity, while knowledge of the catalytic mechanism - including limiting and synergistic steps - is crucial for reliable data interpretation. Enzyme catalysis and specificity cannot be reduced solely to the formation of an encountered complex that makes the reaction between two partners more likely. I highlight how reactants promote conformational changes that significantly contribute to the final specificity and whose impact can only be assessed using kinetic approaches. There is also a need to integrate data with in vivo availability of each competing substrate, and protein data resources must be regularly updated to validate any PTM discovery. These conclusions apply to the substrate specificity of any catalyst.