Widespread Perturbation of Function, Structure, and Dynamics by a Conservative Single-Atom Substitution in Thymidylate Synthase
journal contributionposted on 2016-09-20, 00:00 authored by Paul J. Sapienza, Andrew L. Lee
Thymidylate synthase (TSase) is responsible for synthesizing the sole de novo source of dTMP in all organisms. TSase is a drug target, and as such, it has been well studied in terms of both structure and reaction mechanism. Cysteine 146 in Escherichia coli TSase is universally conserved because it serves as the nucleophile in the enzyme mechanism. Here we use the C146S mutation to probe the role of the sulfur atom in early events in the catalytic cycle beyond serving as the nucleophile. Surprisingly, the single-atom substitution severely decreases substrate binding affinity, and the unfavorable ΔΔG°bind is comprised of roughly equal enthalpic and entropic components at 25 °C. Chemical shifts in the free and dUMP-bound states show the mutation causes perturbations throughout TSase, including regions important for complex stability, in agreement with a less favorable enthalpy change. We measured the nuclear magnetic resonance methyl symmetry axis order parameter (S2axis), a proxy for conformational entropy, for TSase at all vertices of the dUMP binding/C146S mutation thermodynamic cycle and found that the calculated TΔΔS°conf is similar in sign and magnitude to the calorimetric TΔΔS°. Further, we ascribed minor resonances in wild-type–dUMP spectra to a state with a covalent bond between Sγ of C146 and C6 of dUMP and find S2axis values are unaffected by covalent bond formation, indicating this reaction step is neutral with respect to ΔS°conf. Lastly, the C146S mutation allowed us to measure cofactor analog binding by isothermal titration calorimetry without the confounding heat signature of covalent bond formation. Raltitrexed binds free and singly bound TSase with similar affinities, yet the two binding events have different enthalpy changes, providing further evidence of communication between the two active sites.
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Escherichia coli TSasecovalent bondΔΔsingle-atom substitutionConservative Single-Atom SubstitutionS γWidespread Perturbationsulfur atomtitration calorimetryThymidylate Synthase Thymidylate synthaseCysteine 146reaction stepenzyme mechanismreaction mechanismresonance methyl symmetry axis order parametermutation causes perturbationsmeasure cofactor analog bindingS 2 axis valuescovalent bond formationentropic componentsheat signaturebinding eventsdrug targetdecreases substrate binding affinitychemical shiftsC 6enthalpy changesC 146S mutationC 146enthalpy changedUMP-bound states show