High-throughput enzymology reveals mutations throughout a phosphatase that decouple catalysis and transition state analog affinity

Abstract Using High-Throughput Microfluidic Enzyme Kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations throughout the Alkaline Phosphatase PafA on binding affinity for two transition state analogs (TSAs), vanadate and tungstate. As predicted by catalytic models invoking transition state complementary, mutations to active site and active site-contacting residues had highly similar impacts on catalysis and TSA binding. Unexpectedly, most mutations to more distal residues which reduced catalysis had little or no impact on TSA binding and many even increased affinity for tungstate. These disparate effects are accounted for by a model in which distal mutations alter the enzyme’s conformational landscape and increase occupancy of microstates that are catalytically less effective but better able to accommodate larger transition state analogs. In support of this model, glycine substitutions (rather than valine) were more likely to increase tungstate affinity, presumably due to increased conformational flexibility and increased occupancy of previously disfavored microstates. These results indicate that residues throughout an enzyme provide specificity for the transition state and discriminate against analogs that are larger only by tenths of an Ångström. Thus, engineering enzymes that rival the most powerful natural enzymes will likely require consideration not just of residues in and around the active site, but also of more distal residues that shape the enzyme’s conformational landscape and finetune the active site. In addition, the extensive functional communication between the active site and remote residues may provide interconnections needed for allostery and make allostery a highly evolvable trait. Significance Statement Transition state analogs (TSAs) resemble fleeting high-energy transition states and have been used to inhibit enzymes in nature and medicine, to learn about enzyme active site features, and to design and select new enzymes. While TSAs mimic transition states, they differ from actual TSs, and we exploit these differences here. Systematic TSA affinity measurements for 1,004 mutants of PafA (a model phosphatase enzyme) revealed effects in and around the active site that mirror their effects on catalysis, but TSA-binding and catalytic effects diverge more distally. These observations suggest that residues throughout an enzyme adjust its conformational landscape on the tenth-Ångström scale to optimize the active site for catalysis, rendering allostery more evolvable in nature but likely complicating enzyme design.

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