1JCS

CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH THE PEPTIDE SUBSTRATE TKCVFM AND AN ANALOG OF FARNESYL DIPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1073/pnas.241407898
  • Primary Citation of Related Structures:  
    1JCQ, 1JCS, 1JCR

  • 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 ...

    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.


    Related Citations: 
    • The Basis for K-Ras4B Binding Specificity to Protein Farnesyltransferase Revealed by 2A Resolution Ternary Complex Structures
      Long, S.B., Casey, P.J., Beese, L.S.
      (2000) Structure 8: 209
    • Crystal Structure of Protein Farnesyltransferase at 2.25A Resolution
      Park, H.-W., Boduluri, S.R., Moomaw, J.F., Casey, P.J., Beese, L.S.
      (1997) Science 275: 1800

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN FARNESYLTRANSFERASE, ALPHA SUBUNITA377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN FARNESYLTRANSFERASE, BETA SUBUNITB437Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SYNTHETIC HEXAPEPTIDE TKCVFMC6N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FII
Query on FII

Download Ideal Coordinates CCD File 
E [auth B][(3,7,11-TRIMETHYL-DODECA-2,6,10-TRIENYLOXYCARBAMOYL)-METHYL]-PHOSPHONIC ACID
C17 H30 N O5 P
JAOBYUCYSAOLHS-XGGJEREUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
F [auth B], G [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.921α = 90
b = 170.921β = 90
c = 69.425γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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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