5V7P

Atomic structure of the eukaryotic intramembrane Ras methyltransferase ICMT (isoprenylcysteine carboxyl methyltransferase), in complex with a monobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT.

Diver, M.M.Pedi, L.Koide, A.Koide, S.Long, S.B.

(2018) Nature 553: 526-529

  • DOI: 10.1038/nature25439
  • Primary Citation of Related Structures:  

  • PubMed 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 r ...

    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 carboxylate. This final step is catalysed by isoprenylcysteine carboxyl methyltransferase (ICMT), a eukaryote-specific integral membrane enzyme that resides in the endoplasmic reticulum. 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 RAS, prelamin A and RAB. Inhibition of ICMT has potential for combating progeria and cancer. 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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-S-isoprenylcysteine O-methyltransferase
A
288Tribolium castaneumMutation(s): 0 
EC: 2.1.1.100
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Methyltransferases
Protein: 
Isoprenylcysteine carboxyl methyltransferase (ICMT) with monobody inhibitor
Find proteins for D6WJ77 (Tribolium castaneum)
Go to UniProtKB:  D6WJ77
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
monobody
D
95N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UND
Query on UND

Download SDF File 
Download CCD File 
A
UNDECANE
LIPID FRAGMENT
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
 Ligand Interaction
MPG
Query on MPG

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Download CCD File 
A
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
D10
Query on D10

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Download CCD File 
A
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.554α = 90.00
b = 87.691β = 90.00
c = 147.681γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHARPphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Type: Database references
  • Version 1.2: 2018-02-07
    Type: Database references