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

Jieyu Zhou, Luying Yang, Alicia DeColli, Caren Freel Meyers, Natalia S. Nemeria, Frank Jordan

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


The enzyme 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) is a key enzyme in the methylerythritol 4-phosphate pathway and is a target for the development of antibiotics, herbicides, and antimalarial drugs. DXPS catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate (DXP), a branch point metabolite in isoprenoid biosynthesis, and is also used in the biosynthesis of thiamin (vitamin B1) and pyridoxal (vitamin B6). Previously, we found that DXPS is unique among the superfamily of thiamin diphosphate (ThDP)-dependent enzymes in stabilizing the predecarboxylation intermediate, C2-alpha-lactyl-thiamin diphosphate (LThDP), which has subsequent decarboxylation that is triggered by D-glyceraldehyde 3-phosphate (GAP). Herein, we applied hydrogen–deuterium (H/D) exchange MS (HDX-MS) of full-length Escherichia coli DXPS to provide a snapshot of the conformational dynamics of this enzyme, leading to the following conclusions. (i) The high sequence coverage of DXPS allowed us to monitor structural changes throughout the entire enzyme, including two segments (spanning residues 183–238 and 292–317) not observed by X-ray crystallography. (ii) Three regions of DXPS (spanning residues 42–58, 183–199, and 278–298) near the active center displayed both EX1 (monomolecular) and EX2 (bimolecuar) H/D exchange (HDX) kinetic behavior in both ligand-free and ligand-bound states. All other peptides behaved according to the common EX2 kinetic mechanism. (iii) The observation of conformational changes on DXPS provides support for the role of conformational dynamics in the DXPS mechanism: The closed conformation of DXPS is critical for stabilization of LThDP, whereas addition of GAP converts DXPS to the open conformation that coincides with decarboxylation of LThDP and DXP release.

Original languageEnglish (US)
Pages (from-to)9355-9360
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number35
StatePublished - Aug 29 2017


  • Conformational dynamics
  • DXP synthase
  • EX1 kinetics
  • H/D exchange MS
  • ThDP-dependent enzymes

ASJC Scopus subject areas

  • General


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