Deciphering the allosteric regulation of mycobacterial inosine-5′-monophosphate dehydrogenase

• Published in: Nature communications 2024-08, Vol.15 (1), p.6673-14, Article 6673
• Main Authors: Bulvas, Ondřej, Knejzlík, Zdeněk, Sýs, Jakub, Filimoněnko, Anatolij, Čížková, Monika, Clarová, Kamila, Rejman, Dominik, Kouba, Tomáš, Pichová, Iva
• Format: Article
• Language: English
• Subjects: 101/28; 101/58; 631/326/41/2536; 631/45/173; 631/535/1258/1259; 82/80; 82/83; Adenine; Adenosine triphosphate; Adenosine Triphosphate - metabolism; Allosteric properties; Allosteric Regulation; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Catalytic Domain; Cryoelectron Microscopy; Dehydrogenase; Dehydrogenases; Enzymes; Guanosine Pentaphosphate - metabolism; Guanosine triphosphate; Guanosine Triphosphate - metabolism; Homeostasis; Humanities and Social Sciences; IMP Dehydrogenase - antagonists & inhibitors; IMP Dehydrogenase - chemistry; IMP Dehydrogenase - metabolism; Inosine monophosphate; Inosine Monophosphate - chemistry; Inosine Monophosphate - metabolism; Models, Molecular; Molecular modelling; multidisciplinary; Mycobacterium smegmatis - enzymology; Mycobacterium smegmatis - metabolism; Nucleotides; Occlusion; Protein Binding; Regulatory mechanisms (biology); Science; Science (multidisciplinary); Substrate inhibition
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-50933-6

Allosteric regulation of inosine 5′-monophosphate dehydrogenase (IMPDH), an essential enzyme of purine metabolism, contributes to the homeostasis of adenine and guanine nucleotides. However, the precise molecular mechanism of IMPDH regulation in bacteria remains unclear. Using biochemical and cryo-EM approaches, we reveal the intricate molecular mechanism of the IMPDH allosteric regulation in mycobacteria. The enzyme is inhibited by both GTP and (p)ppGpp, which bind to the regulatory CBS domains and, via interactions with basic residues in hinge regions, lock the catalytic core domains in a compressed conformation. This results in occlusion of inosine monophosphate (IMP) substrate binding to the active site and, ultimately, inhibition of the enzyme. The GTP and (p)ppGpp allosteric effectors bind to their dedicated sites but stabilize the compressed octamer by a common mechanism. Inhibition is relieved by the competitive displacement of GTP or (p)ppGpp by ATP allowing IMP-induced enzyme expansion. The structural knowledge and mechanistic understanding presented here open up new possibilities for the development of allosteric inhibitors with antibacterial potential. Here, Bulvas et al use biochemical and cryo-EM techniques to profile the regulatory mechanisms of the essential mycobacterial enzyme IMPDH. They show how GTP and (p)ppGpp nucleotides inhibit IMPDH by locking it in an inactive state.