A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases

Abstract

Inosine-5′-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of regulation remain largely unknown. Using the enzyme from the industrial fungus Ashbya gossypii, we demonstrate that the binding of adenine and guanine nucleotides to the canonical nucleotide binding sites of the regulatory Bateman domain induces different enzyme conformations with significantly distinct catalytic activities. Thereby, the comparison of their high-resolution structures defines the mechanistic and structural details of a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity of eukaryotic IMPDHs. Remarkably, retinopathy-associated mutations lie within the mechanical hinges of the conformational change, highlighting its physiological relevance. Our results expand the mechanistic repertoire of Bateman domains and pave the road to new approaches targeting IMPDHs.

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

“…There is strong density at both of the canonical ATP-binding sites within the Bateman domain (Fig. 3F), consistent with previous crystal structures of ATP/ADP-bound fungal and bacterial IMPDH (Buey et al 2017; Labesse et al 2013).…”

“…We and others previously reported that GTP can stabilize compressed IMPDH2 filaments or drive their disassembly, depending on what other ligands are present (Buey et al 2017; Anthony et al 2017; Duong-Ly et al 2018). To understand how ligand status of the active site tunes the response to GTP, we systematically explored the effects of different ligand combinations on filament assembly.…”

“…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.…”

T Cell Activation Triggers Reversible Inosine-5'-Monophosphate Dehydrogenase Assembly

“…These observations are best explained by the conversion of exogenous guanosine to form unlabeled GMP, GDP and GTP. GMP directly inhibits IMPDH catalytic activity competitively with the substrate IMP (Gilbert et al, 1979) while GDP and GTP inhibit IMPDH allosterically by promoting the catalytically inactive, collapsed conformation of IMPDH (Anthony et al, 2017;Buey et al). Guanine nucleotides are also known to exert feedback control at two additional points in purine biosynthesis; GMP inhibits the synthesis of phosphoribosyl pyrophosphate in the rate-limiting first step of purine biosynthesis and GTP is a co-factor required by adenylosuccinate synthase activity to divert IMP toward adenine nucleotide biosynthesis ( Figure 4A).…”