Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT

The X-ray structure of the integral membrane protein isoprenylcysteine carboxyl methyltransferase suggests mechanisms by which it recognizes both water-soluble and membrane-bound reactants to catalyze the methylation of RAS and other CAAX proteins at the membrane-cytosol interface. Isoprenylcysteine carboxyl methyltransferase (ICMT) is a eukaryotic membrane-embedded enzyme. ICMT methylates the exposed prenylcysteine residue of RAS GTPases and other CAAX proteins during their processing in the endoplasmic reticulum membrane. Stephen Long and colleagues determine the crystal structure of ICMT in an environment akin to a lipid membrane and in complex with a monobody inhibitor, a cofactor and a lipid molecule that mimics the prenylated substrate. The active site of ICMT spans cytosolic and membrane regions, and the structure indicates how the enzyme brings together the cytosolic methyl donor and the membrane-associated substrate. Inhibition of ICMT is a potential therapeutic strategy against progeria and cancer, and these structural findings should inform the rational design of small-molecule modulators. The maturation of RAS GTPases and approximately 200 other cellular CAAX proteins involves three enzymatic steps: addition of a farnesyl or geranylgeranyl prenyl lipid to the cysteine (C) in the C-terminal CAAX motif, proteolytic cleavage of the AAX residues and methylation of the exposed prenylcysteine residue at its terminal carboxylate1. This final step is catalysed by isoprenylcysteine carboxyl methyltransferase (ICMT), a eukaryote-specific integral membrane enzyme that resides in the endoplasmic reticulum2. ICMT is the only cellular enzyme that is known to methylate prenylcysteine substrates; methylation is important for the biological functions of these substrates, such as the membrane localization and subsequent activity of RAS1, prelamin A3 and RAB4. Inhibition of ICMT has potential for combating progeria3 and cancer5,6,7,8. Here we present an X-ray structure of ICMT, in complex with its cofactor, an ordered lipid molecule and a monobody inhibitor, at 2.3 Å resolution. The active site spans cytosolic and membrane-exposed regions, indicating distinct entry routes for the cytosolic methyl donor, S-adenosyl-l-methionine, and for prenylcysteine substrates, which are associated with the endoplasmic reticulum membrane. The structure suggests how ICMT overcomes the topographical challenge and unfavourable energetics of bringing two reactants that have different cellular localizations together in a membrane environment—a relatively uncharacterized but defining feature of many integral membrane enzymes.