Evolutionary and Structural Constraints Define a Mutation-Resistant Catalytic Core in E. coli Serine Hydroxy methyltransferase (SHMT)

Abstract

Serine hydroxymethyltransferase is an essential enzyme in the Escherichia coli folate pathway, yet it has not been adopted as an antibacterial target, unlike DHFR, DHPS, or thymidylate synthase. To investigate this discrepancy, we applied a multi-scale computational framework that integrates large-scale sequence analysis of 1000 homologs, coevolutionary interaction mapping, structural community analysis, intrinsic disorder profiling, and adaptive fitness modelling. These analyses converge on a single conclusion: the catalytic core of SHMT forms an exceptionally conserved and tightly coupled structural unit. This region exhibits dense coevolution, strong intramolecular connectivity, minimal disorder, and extremely low mutational tolerance. Peripheral loops and termini, in contrast, are far more flexible. Relative to established folate-pathway antibiotic targets, SHMT active site is even more rigid and evolutionarily constrained. This extreme constraint may limit the emergence of resistance-compatible mutations, providing a plausible explanation for the absence of natural-product inhibitors. Fitness trajectory modelling supports this interpretation, showing that nearly all active-site residues tolerate only rare or neutral substitutions. Together, these findings identify SHMT as a structurally stable and evolutionarily restricted enzyme whose catalytic architecture is unusually protected. This makes SHMT an underexplored yet promising target for the rational design of next-generation antibacterial agents.