1KZO

PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYLATED K-RAS4B PEPTIDE PRODUCT AND FARNESYL DIPHOSPHATE SUBSTRATE BOUND SIMULTANEOUSLY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Reaction Path of Protein Farnesyltransferase at Atomic Resolution

Long, S.B.Casey, P.J.Beese, L.S.

(2002) Nature 419: 645-650

  • DOI: 10.1038/nature00986
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein farnesyltransferase (FTase) catalyses the attachment of a farnesyl lipid group to numerous essential signal transduction proteins, including members of the Ras superfamily. The farnesylation of Ras oncoproteins, which are associated with 30% ...

    Protein farnesyltransferase (FTase) catalyses the attachment of a farnesyl lipid group to numerous essential signal transduction proteins, including members of the Ras superfamily. The farnesylation of Ras oncoproteins, which are associated with 30% of human cancers, is essential for their transforming activity. FTase inhibitors are currently in clinical trials for the treatment of cancer. Here we present a complete series of structures representing the major steps along the reaction coordinate of this enzyme. From these observations can be deduced the determinants of substrate specificity and an unusual mechanism in which product release requires binding of substrate, analogous to classically processive enzymes. A structural model for the transition state consistent with previous mechanistic studies was also constructed. The processive nature of the reaction suggests the structural basis for the successive addition of two prenyl groups to Rab proteins by the homologous enzyme geranylgeranyltransferase type-II. Finally, known FTase inhibitors seem to differ in their mechanism of inhibiting the enzyme.


    Related Citations: 
    • Co-Crystal Structure of Mammalian Protein Farnesyltransferase with a Farnesyl Diphosphate Substrate
      Long, S.B.,Casey, P.J.,Beese, L.S.
      (1998) Biochemistry 37: 9612
    • 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, North Carolina 27710, USA. lsb@biochem.duke.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein Farnesyltransferase alpha subunit
A
377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.58, 2.5.1.59
Find proteins for Q04631 (Rattus norvegicus)
Go to UniProtKB:  Q04631
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein Farnesyltransferase beta subunit
B
437Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
Find proteins for Q02293 (Rattus norvegicus)
Go to UniProtKB:  Q02293
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Farnesylated K-Ras4B peptide product
C
11Homo sapiensMutation(s): 0 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAR
Query on FAR

Download SDF File 
Download CCD File 
C
FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FPP
Query on FPP

Download SDF File 
Download CCD File 
B
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FPPKd: 5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.159 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 171.199α = 90.00
b = 171.199β = 90.00
c = 69.444γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance