1KZO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.159 
  • R-Value Observed: 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
  • Structures With Same Primary Citation

  • 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: 
    • 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
    • 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

    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 subunitA377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.21 (PDB Primary Data), 2.5.1.58 (UniProt), 2.5.1.59 (UniProt)
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein Farnesyltransferase beta subunitB437Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.21 (PDB Primary Data), 2.5.1.58 (UniProt)
Find proteins for Q02293 (Rattus norvegicus)
Explore Q02293 
Go to UniProtKB:  Q02293
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Farnesylated K-Ras4B peptide productC11N/AMutation(s): 0 
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS  P01116
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FPP
Query on FPP

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

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

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B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.199α = 90
b = 171.199β = 90
c = 69.444γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    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