Fig. 4: IMP binding induces reorganization of the MsmIMPDH active site and subsequent dissolution of the tetramer dimerization interface.

a The binding of IMP (in green) induces movement of the Cys-loop (residues 320–326, in orange) from an open conformation to a closed conformation. b The initial part of the flap loop (residues 405–415, in purple) interacts with IMP through residues Tyr405, Met408, and Gly409. The contacts are depicted by the grey dotted lines; each number indicates the distance in Å. c IMP binding induces a movement of about 3.5 Å of the entire finger loop (residues 391–404 in red), as indicated by the red arrows. d The two-dimensional representation shows the contacts between IMP and residues forming the MsmIMPDH active site. e Changes to the finger (in red), flap (in purple), and Cys-loop (in orange) after IMP binding (green spheres) lead to extensive rearrangement of the tetramer–tetramer interface, enabling octamer expansion. For consistency, the ATP-bound MsmIMPDH structure was chosen as the model for the compressed conformation across all panels (grey cartoon in a–c). f SAXS profiles of 56 µM MsmIMPDH show the effect of nucleotides on the quaternary structure. For ease of visualization, plots are conveniently displaced along the y axis to represent the three obtained conformations: (green) tetramers induced by 10 mM IMP; (orange) compressed octamers in the apo state, (red) with 10 mM GTP, and (blue) with 10 mM ATP; and (purple) extended octamers induced by 10 mM ATP and IMP. Dashed lines show the theoretical SAXS profiles calculated from the respective cryo-EM structures fitted to the experimental scattering curves. The curve fitted to the IMP dataset (marked by *) represents a 75:25% mixture of tetramers and octamers, while the fit for the ATP + IMP dataset (marked by **) indicates a 38:62% mixture of compressed and extended conformations, as calculated using the OLIGOMER program⁵³. g Mass photometry profiles of 20 nM MsmIMPDH in its apo state and in the presence of 5 mM ATP and/or IMP reveal two distinct peaks. The observed particle masses of the first and second peaks correspond with the MsmIMPDH tetramer (213.2 kDa) and octamer (426.4 kDa).