A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity

Abstract

IMP dehydrogenase (IMPDH) catalyzes the rate-limiting step in the de novo GTP biosynthetic pathway and plays essential roles in cell proliferation. As a clinical target, IMPDH has been studied for decades but it has only been within the last years that we are starting to understand the complexity of the mechanisms of its physiological regulation. Here, we report structural and functional insights into how adenine and guanine nucleotides control a conformational switch that modulates the assembly of the two human IMPDHs into cytoophidia and allosterically regulates their catalytic activity. In vitro reconstituted micron-length cytoophidia show catalytic activity comparable to unassembled IMPDH but, in turn, are more resistant to GTP/GDP allosteric inhibition. Therefore, IMPDH cytoophidia formation facilitates the accumulation of high levels of guanine nucleotides when the cell requires it. Finally, we demonstrate that most of the IMPDH retinopathy-associated mutations abrogate GTP/GDP-induced allosteric inhibition and alter cytoophidia dynamics.

Ensemble cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation

“…4E, S6D-F, Table 5). This octamer is conformationally similar (backbone RMSD = 0.978 Å) to a recent higher-resolution crystal structure of IMPDH2 bound to GTP (PDB 6i0o) (Buey et al 2017; Fernández-Justel et al 2019). The Bateman domains are fully compressed with three occupied allosteric sites.…”

“…The N-terminal tail of IMPDH, corresponding to residues 1-28 in IMPDH2, is the least conserved part of the protein, with large variation in length and sequence between phyla, as well as conformational variation among known structures (Fig. S3A) (Trapero et al 2018; Makowska-Grzyska et al 2015; Kim et al 2017; Prosise & Luecke 2003; Osipiuk et al 2014; Labesse et al 2013; Buey, Ledesma-Amaro, Balsera, et al 2015; Fernández-Justel et al 2019). The residues involved in filament contacts, however, are conserved among chordates, consistent with the fact that IMPDH polymerization has only been reported in vertebrates (Fig.…”

“…In eukaryotes, adenine and guanine nucleotides allosterically modulate IMPDH activity by altering oligomeric state (Buey et al 2017; Fernández-Justel et al 2019). IMPDH tetramers reversibly assemble into octamers when nucleotides bind the two canonical sites and drive dimerization of Bateman domains (Fig 1C).…”

“…GTP/GDP binding induces a compressed conformation by changing the relative orientation of the two domains. This brings the active sites of opposing tetramers tightly together, forming an interdigitated pseudo beta-barrel that prevents reopening and product release and inhibits IMPDH activity by a mechanism described as a “conformational switch” between extended and compressed states (Buey, Ledesma-Amaro, Velázquez-Campoy, et al 2015; Buey et al 2017; Fernández-Justel et al 2019). Because inhibition requires interactions between two opposing tetramers, this switch is functionally relevant in only the octameric state.…”

“…In vitro treatment with ATP or GTP induces assembly of human IMPDH into filaments composed of stacked octamers interacting through their catalytic domains (Fig. 1D) (Labesse et al 2013; Anthony et al 2017; Fernández-Justel et al 2019). Filament segments can both extend and compress, and assembly does not have a direct effect on the activity of IMPDH2 (Anthony et al 2017).…”