1O1R

Structure of FPT bound to GGPP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Biochemical and Structural Studies with Prenyl Diphosphate Analogues Provide Insights into Isoprenoid Recognition by Protein Farnesyl Transferase

Turek-Etienne, T.C., Strickland, C.L., Distefano, M.D.

(2003) Biochemistry 42: 3716-3724

  • DOI: 10.1021/bi0266838
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Protein farnesyl transferase (PFTase) catalyzes the reaction between farnesyl diphosphate and a protein substrate to form a thioether-linked prenylated protein. The fact that many prenylated proteins are involved in signaling processes has generated ...

    Protein farnesyl transferase (PFTase) catalyzes the reaction between farnesyl diphosphate and a protein substrate to form a thioether-linked prenylated protein. The fact that many prenylated proteins are involved in signaling processes has generated considerable interest in protein prenyl transferases as possible anticancer targets. While considerable progress has been made in understanding how prenyl transferases distinguish between related target proteins, the rules for isoprenoid discrimination by these enzymes are less well understood. To clarify how PFTase discriminates between FPP and larger prenyl diphosphates, we have examined the interactions between the enzyme and several isoprenoid analogues, GGPP, and the farnesylated peptide product using a combination of biochemical and structural methods. Two photoactive isoprenoid analogues were shown to inhibit yeast PFTase with K(I) values as low as 45 nM. Crystallographic analysis of one of these analogues bound to PFTase reveals that the diphosphate moiety and the two isoprene units bind in the same positions occupied by the corresponding atoms in FPP when bound to PFTase. However, the benzophenone group protrudes into the acceptor protein binding site and prevents the binding of the second (protein) substrate. Crystallographic analysis of geranylgeranyl diphosphate bound to PFTase shows that the terminal two isoprene units and diphosphate group of the molecule map to the corresponding atoms in FPP; however, the first and second isoprene units bulge away from the acceptor protein binding site. Comparison of the GGPP binding mode with the binding of the farnesylated peptide product suggests that the bulkier isoprenoid cannot rearrange to convert to product without unfavorable steric interactions with the acceptor protein. Taken together, these data do not support the "molecular ruler hypotheses". Instead, we propose a "second site exclusion model" in which PFTase binds larger isoprenoids in a fashion that prevents the subsequent productive binding of the acceptor protein or its conversion to product.

    Organizational Affiliation: 

    Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase alpha subunit
A
380Rattus 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
427Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
Find proteins for Q02293 (Rattus norvegicus)
Go to UniProtKB:  Q02293
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GRG
Query on GRG
Download SDF File 
Download CCD File 
B
GERANYLGERANYL DIPHOSPHATE
C20 H36 O7 P2
OINNEUNVOZHBOX-QIRCYJPOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.177 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 171.650α = 90.00
b = 171.650β = 90.00
c = 69.080γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description