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: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/nature25439
  • Primary Citation of Related Structures:  
    5V7P, 5VG9

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-S-isoprenylcysteine O-methyltransferase288Tribolium castaneumMutation(s): 0 
Gene Names: TcasGA2_TC013078
EC: 2.1.1.100
Membrane Entity: Yes 
UniProt
Find proteins for D6WJ77 (Tribolium castaneum)
Explore D6WJ77 
Go to UniProtKB:  D6WJ77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6WJ77
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
monobodyB [auth D]95synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
MPG
Query on MPG

Download Ideal Coordinates CCD File 
AA [auth A]
R [auth A]
S [auth A]
T [auth A]
U [auth A]
AA [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
UND
Query on UND

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth A]
UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.554α = 90
b = 87.691β = 90
c = 147.681γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references