Letter

Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT

  • Nature volume 553, pages 526529 (25 January 2018)
  • doi:10.1038/nature25439
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Abstract

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.

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Acknowledgements

We thank D. Julius, C. D. Lima, M. Luo, N. P. Pavletich, R. K. Hite, S. Shuman and members of the Long laboratory for discussions. Beamlines 24-ID and 23-ID at the Advanced Photon Source are supported by NIH grants ACB-12002, AGM-12006, P41 GM103403 and S10 RR029205, under DOE contract DE-AC02-06CH11357. This work was supported, in part, by an American Heart Association Pre-doctoral Fellowship (M.M.D.), a Burroughs Wellcome Career Award (S.B.L), the Geoffrey Beene Cancer Research Center at MSKCC (S.B.L.), a core-facilities support grant to MSKCC (P30 CA008748) and NIH grant U54-GM087519 (S.K.).

Author information

Author notes

    • Melinda M. Diver

    Present address: Department of Physiology, University of California, San Francisco, San Francisco, California 94158, USA.

Affiliations

  1. Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA

    • Melinda M. Diver
    • , Leanne Pedi
    •  & Stephen B. Long
  2. Graduate Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Medicine Graduate School of Medical Sciences, 1300 York Avenue, New York, New York 10065, USA

    • Melinda M. Diver
  3. Perlmutter Cancer Center, New York University Langone Medical Center, 430 East 29th Street, New York, New York 10016, USA

    • Akiko Koide
    •  & Shohei Koide
  4. Department of Medicine, New York University Langone Medical Center, 430 East 29th Street, New York, New York 10016, USA

    • Akiko Koide
  5. Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, 430 East 29th Street, New York, New York 10016, USA

    • Shohei Koide

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Contributions

M.M.D. and L.P. cloned, expressed and purified proteins. A.K. and S.K. developed monobodies. M.M.D. performed all other experiments. M.M.D. and S.B.L. designed experiments, determined structures, analysed results and prepared the manuscript with contributions from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Stephen B. Long.

Reviewer Information Nature thanks M. Bergö, P. Casey and O. Nureki for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Figure 1

    The uncropped scan of the Western blot in Extended Data Figure 6b. The boxed regions are displayed in Extended Data Figure 6b. The band at ~ 28 kDa corresponds to PreScission protease, which contains a His-tag. Lanes that are not boxed are not relevant to this experiment.

  2. 2.

    Life Sciences Reporting Summary

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