1O1R

Structure of FPT bound to GGPP

DOI: 10.2210/pdb1O1R/pdb

Classification: TRANSFERASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-01-14 Released: 2003-05-06
Deposition Author(s): Turek-Etienne, T.C., Strickland, C.L., Distefano, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Work: 0.177
R-Value Observed: 0.177

wwPDB Validation3D 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

PubMed: 12667062 Search on PubMed
DOI: 10.1021/bi0266838
Structures With Same Primary Citation

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 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
Molecule	Chains	Sequence Length	Organism	Details
Protein farnesyltransferase alpha subunit	A	380	Rattus norvegicus	Mutation(s): 0 Gene Names: Fnta EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt), 2.5.1.59 (UniProt)
Find proteins for Q04631 (Rattus norvegicus) Go to UniProtKB: Q04631
Protein Feature View Full Protein Feature View for Q04631

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Protein farnesyltransferase beta subunit	B	427	Rattus norvegicus	Mutation(s): 0 Gene Names: Fntb EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt)
Find proteins for Q02293 (Rattus norvegicus) Go to UniProtKB: Q02293
Protein Feature View Full Protein Feature View for Q02293

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GRG Query on GRG Download CCD File	B	GERANYLGERANYL DIPHOSPHATE C₂₀ H₃₆ O₇ P₂ OINNEUNVOZHBOX-QIRCYJPOSA-N		Ligand Interaction
ZN Query on ZN Download CCD File	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction