Crystal structure of NRAS Q61K with a ligand-induced pocket near switch II

Eur J Cell Biol. 2024 Jun;103(2):151414. doi: 10.1016/j.ejcb.2024.151414. Epub 2024 Apr 15.

Abstract

The RAS isoforms (KRAS, HRAS and NRAS) have distinct cancer type-specific profiles. NRAS mutations are the second most prevalent RAS mutations in skin and hematological malignancies. Although RAS proteins were considered undruggable for decades, isoform and mutation-specific investigations have produced successful RAS inhibitors that are either specific to certain mutants, isoforms (pan-KRAS) or target all RAS proteins (pan-RAS). While extensive structural and biochemical investigations have focused mainly on K- and H-RAS mutations, NRAS mutations have received less attention, and the most prevalent NRAS mutations in human cancers, Q61K and Q61R, are rare in K- and H-RAS. This manuscript presents a crystal structure of the NRAS Q61K mutant in the GTP-bound form. Our structure reveals a previously unseen pocket near switch II induced by the binding of a ligand to the active form of the protein. This observation reveals a binding site that can potentially be exploited for development of inhibitors against mutant NRAS. Furthermore, the well-resolved catalytic site of this GTPase bound to native GTP provides insight into the stalled GTP hydrolysis observed for NRAS-Q61K.

Keywords: Crystal structure; Induced fit; NRAS; Oncogenic mutation; RAS superfamily small GTPases.

MeSH terms

  • Crystallography, X-Ray
  • GTP Phosphohydrolases* / chemistry
  • GTP Phosphohydrolases* / genetics
  • GTP Phosphohydrolases* / metabolism
  • Guanosine Triphosphate* / metabolism
  • Humans
  • Ligands
  • Membrane Proteins* / chemistry
  • Membrane Proteins* / genetics
  • Membrane Proteins* / metabolism
  • Models, Molecular
  • Mutation

Substances

  • GTP Phosphohydrolases
  • Membrane Proteins
  • NRAS protein, human
  • Guanosine Triphosphate
  • Ligands