Human isocitrate dehydrogenase 1 (IDH1) is a highly conserved
metabolic
enzyme that catalyzes the interconversion of isocitrate and α-ketoglutarate.
Kinetic and structural studies with IDH1 have revealed evidence of
striking conformational changes that occur upon binding of its substrates,
isocitrate and NADP+, and its catalytic metal cation. Here,
we used hydrogen–deuterium exchange mass spectrometry (HDX-MS)
to build a comprehensive map of the dynamic conformational changes
experienced by IDH1 upon ligand binding. IDH1 proved well-suited for
HDX-MS analysis, allowing us to capture profound changes in solvent
accessibility at substrate binding sites and at a known regulatory
region, as well as at more distant local subdomains that appear to
support closure of this protein into its active conformation. HDX-MS
analysis suggested that IDH1 is primarily purified with NADP(H) bound
in the absence of its metal cation. Subsequent metal cation binding,
even in the absence of isocitrate, was critical for driving large
conformational changes. WT IDH1 folded into its fully closed conformation
only when the full complement of substrates and metal was present.
Finally, we show evidence supporting a previously hypothesized partially
open conformation that forms prior to the catalytically active state,
and we propose this conformation is driven by isocitrate binding in
the absence of metal.
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