The Relationship between Enzyme Conformational Change, Proton Transfer, and Phosphoryl Transfer in β‑Phosphoglucomutase
datasetposted on 2021-10-07, 17:45 authored by Angus J. Robertson, Alex L. Wilson, Matthew J. Burn, Matthew J. Cliff, Paul L. A. Popelier, Jonathan P. Waltho
Molecular details for the timing and role of proton transfer in phosphoryl transfer reactions are poorly understood. Here, we have combined QM models, experimental NMR measurements, and X-ray structures to establish that the transition of an archetypal phosphoryl transfer enzyme, βPGM, from a very closed near-attack conformation to a fully closed transition state analogue (TSA) conformation triggers both partial proton transfer from the general acid–base residue to the leaving group oxygen and partial dissociation of the transferring phosphoryl group from the leaving group oxygen. Proton transfer continues but is not completed throughout the reaction path of the phosphoryl transfer with the enzyme in the TSA conformation. Moreover, using interacting quantum atoms (IQA) and relative energy gradient (REG) analysis approaches, we observed that the change in the position of the proton and the corresponding increased electrostatic repulsion between the proton and the phosphorus atom provide a stimulus for phosphoryl transfer in tandem with a reduction in the negative charge density on the leaving group oxygen atom. The agreement between solution-phase 19F NMR measurements and equivalent QM models of βPGMWT and βPGMD10N TSA complexes confirms the protonation state of G6P in the two variants, validating the employed QM models. Furthermore, QM model predictions of an AlF4 distortion in response to the proton position are confirmed using high resolution X-ray crystal structures, not only providing additional validation to the QM models but also further establishing metal fluorides as highly sensitive experimental predictors of active-site charge density distributions.
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relative energy gradientproviding additional validationphosphorus atom providenegative charge densityleaving group oxygenf nmr measurementsexperimental nmr measurementsestablishing metal fluoridesqm model predictionstransferring phosphoryl groupequivalent qm modelsemployed qm modelscombined qm modelswt subd10n sub4 subphosphoryl transfer reactionstsa complexes confirmsray crystal structures19 supproton transfer continuespartial proton transferenzyme conformational changeqm modelsphosphoryl transferray structuresproton transferpartial dissociationtwo variantstsa conformationreaction pathprotonation statepoorly understoodconformation triggerscompleted throughoutclosed nearattack conformationanalysis approaches