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

International audienceEstablishing the protein posttranslational modification (PTM) landscape at the proteome scale relieson the target specificity of the relevant enzyme catalysts. Su et al. (ACS Catal, 2021:14877) proposedthat “the kcat/Km value is not the best parameter to determine the in vivo substrate specificity of anenzyme. Instead, the binding affinities of substrates are more important for determining the substratespecificity 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 discussionof the relative merits of different approaches used to identify protein modification targets. My point ofview 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 forreliable data interpretation. Enzyme catalysis and specificity cannot be reduced solely to the formationof an encountered complex that makes the reaction between two partners more likely. I highlight howreactants promote conformational changes that significantly contribute to the final specificity andwhose impact can only be assessed using kinetic approaches. There is also a need to integrate data within vivo availability of each competing substrate, and protein data resources must be regularly updatedto validate any PTM discovery. These conclusions apply to the substrate specificity of any catalyst