1JCR

CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH THE NON-SUBSTRATE TETRAPEPTIDE INHIBITOR CVFM AND FARNESYL DIPHOSPHATE SUBSTRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The crystal structure of human protein farnesyltransferase reveals the basis for inhibition by CaaX tetrapeptides and their mimetics.

Long, S.B.Hancock, P.J.Kral, A.M.Hellinga, H.W.Beese, L.S.

(2001) Proc Natl Acad Sci U S A 98: 12948-12953

  • DOI: https://doi.org/10.1073/pnas.241407898
  • Primary Citation of Related Structures:  
    1JCQ, 1JCR, 1JCS

  • PubMed Abstract: 

    Protein farnesyltransferase (FTase) catalyzes the attachment of a farnesyl lipid group to the cysteine residue located in the C-terminal tetrapeptide of many essential signal transduction proteins, including members of the Ras superfamily. Farnesylation is essential both for normal functioning of these proteins, and for the transforming activity of oncogenic mutants. Consequently FTase is an important target for anti-cancer therapeutics. Several FTase inhibitors are currently undergoing clinical trials for cancer treatment. Here, we present the crystal structure of human FTase, as well as ternary complexes with the TKCVFM hexapeptide substrate, CVFM non-substrate tetrapeptide, and L-739,750 peptidomimetic with either farnesyl diphosphate (FPP), or a nonreactive analogue. These structures reveal the structural mechanism of FTase inhibition. Some CaaX tetrapeptide inhibitors are not farnesylated, and are more effective inhibitors than farnesylated CaaX tetrapeptides. CVFM and L-739,750 are not farnesylated, because these inhibitors bind in a conformation that is distinct from the TKCVFM hexapeptide substrate. This non-substrate binding mode is stabilized by an ion pair between the peptide N terminus and the alpha-phosphate of the FPP substrate. Conformational mapping calculations reveal the basis for the sequence specificity in the third position of the CaaX motif that determines whether a tetrapeptide is a substrate or non-substrate. The presence of beta-branched amino acids in this position prevents formation of the non-substrate conformation; all other aliphatic amino acids in this position are predicted to form the non-substrate conformation, provided their N terminus is available to bind to the FPP alpha-phosphate. These results may facilitate further development of FTase inhibitors.


  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN FARNESYLTRANSFERASE, ALPHA SUBUNIT377Rattus norvegicusMutation(s): 0 
EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt), 2.5.1.59 (UniProt)
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN FARNESYLTRANSFERASE, BETA SUBUNIT437Rattus norvegicusMutation(s): 0 
EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt)
UniProt
Find proteins for Q02293 (Rattus norvegicus)
Explore Q02293 
Go to UniProtKB:  Q02293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02293
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SYNTHETIC TETRAPEPTIDE CVFM4N/AMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.225α = 90
b = 171.225β = 90
c = 69.332γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description