Conformational dynamics of 1-deoxy- d -xylulose 5-phosphate synthase on ligand binding revealed by H/D exchange MS

Significance We applied hydrogen–deuterium exchange MS to a study of full-length Escherichia coli 1-deoxy- d -xylulose 5-phosphate synthase (DXPS), a key enzyme in the methylerythritol 4-phosphate pathway, to provide a snapshot of its conformational dynamics. The three regions displaying an EX1 (monomolecular) exchange behavior, two of which are absent in the X-ray structure, were shown to be dynamic. Open and closed conformations of those regions were revealed with no ligand bound; with substrate analogue bound, a closed conformation was favored, while addition of the second substrate d -glyceraldehyde 3-phosphate and product 1-deoxy- d -xylulose 5-phosphate induced the open conformation, suggesting crucial roles of conformational changes in the mechanism. Our findings revealed a role for active center loops on DXPS, a mechanistically unique thiamin diphosphate-dependent enzyme.