Protein farnesyltransferase
Farnesyltransferase (FTase) is an important zinc metalloenzyme that is responsible for the specific transfer of a 15 carbon isoprenoid farnesyl from farnesyldiphosphate (FPP) to peptide substrates containing a characteristic carboxy-terminal CAAX motif. Within the motif, C is the cysteine that is farnesylated, 'A' represents an aliphatic residue and X is the terminal residue, normally methionine, serine, alanine or glutamine. Much research has been carried out on FTase since the group of substrate peptides it farnesylates includes the Ras family of proteins, the oncogenic forms of which are implicated in cell transformation.
Reference Protein and Structure
- Sequences
-
Q04631
(2.5.1.58, 2.5.1.59)
Q02293 (2.5.1.58)
P01116 (3.6.5.2)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Rattus norvegicus (Norway rat)
- PDB
-
1d8d
- CO-CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A K-RAS4B PEPTIDE SUBSTRATE AND FPP ANALOG AT 2.0A RESOLUTION
(2.0 Å)
- Catalytic CATH Domains
-
1.25.40.120
1.50.10.20
(see all for 1d8d)
- Cofactors
- Magnesium(2+) (1), Zinc(2+) (1)
Enzyme Mechanism
Introduction
The difficulty in obtaining experimental evidence for the mechanism of FTase has led to increased interest in computation studies of the enzyme. A quantum mechanical active-site model has elucidated key transition states of the reaction, and allowed the first description of the mechanism.
The farnesylation of the cysteine residue from the peptide substrate is thought to proceed via a concerted associative mechanism, with partial dissociative character, as previously postulated form experimental studies. The FPP unit attacks the peptide Cys sulphur, forming a covalent bond to the residue and displacing the Zn metal. The metal centre is crucial in polarising the S-C bond, enhancing its electrophilic character.
The free coordination site left on the Zn is filled by the second carboxylate of the metal binding Asp297(B). The divalent magnesium cation present is proposed to stabilise the build up of negative charge on the diphosphate moiety and is implicated in activating the leaving group.
Catalytic Residues Roles
| UniProt | PDB* (1d8d) | ||
| His248, Arg291, Lys294 | His248B, Arg291B, Lys294B | Binds and stabilises the negatively charged phosphate group of the isoprenoid substrate. | electrostatic stabiliser |
| Lys164 | Lys164A | Stabilises the negative charge on the alpha phosphate. | electrostatic stabiliser |
| Asp297, Cys299, His362 | Asp297B, Cys299B, His362B | Forms the zinc binding site in the beta subunit. | metal ligand |
| Asp359 | Asp359B | Asp-359 effects Zn(II) binding through a hydrogen bonding interaction with His362. | electrostatic stabiliser |
| Asp352 | Asp352B | Forms part of the Mg(II) binding site. | metal ligand |
| Tyr300 | Tyr300B | Stabilizes the developing negative charge on the bridging oxygen between the alpha-phosphate and the C1 atom. | electrostatic stabiliser |
Chemical Components
References
- Sousa SF et al. (2009), Chemistry, 15, 4243-4247. The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase. DOI:10.1002/chem.200802745. PMID:19301336.
- Yang Y et al. (2010), Biochemistry, 49, 9658-9666. Finding a Needle in the Haystack: Computational Modeling of Mg2+Binding in the Active Site of Protein Farnesyltransferase. DOI:10.1021/bi1008358. PMID:20923173.
- Sousa SF et al. (2008), J Phys Chem B, 112, 8681-8691. Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation. DOI:10.1021/jp711214j. PMID:18572907.
- Cui G et al. (2007), Biochemistry, 46, 12375-12381. Computational Studies of the Farnesyltransferase Ternary Complex Part II: The Conformational Activation of Farnesyldiphosphate†. DOI:10.1021/bi701324t. PMID:17918965.
- Cui G et al. (2005), Biochemistry, 44, 16513-16523. Computational Studies of the Farnesyltransferase Ternary Complex Part I: Substrate Binding†. DOI:10.1021/bi051020m. PMID:16342942.
- Maurer-Stroh S et al. (2003), Genome Biol, 4, 212-. Protein prenyltransferases. PMID:12702202.
- Long SB et al. (2002), Nature, 419, 645-650. Reaction path of protein farnesyltransferase at atomic resolution. DOI:10.1038/nature00986. PMID:12374986.
- Long SB et al. (2000), Structure, 8, 209-222. The basis for K-Ras4B binding specificity to protein farnesyltransferase revealed by 2 A resolution ternary complex structures. PMID:10673434.
- Long SB et al. (1998), Biochemistry, 37, 9612-9618. Cocrystal Structure of Protein Farnesyltransferase Complexed with a Farnesyl Diphosphate Substrate†,‡. DOI:10.1021/bi980708e. PMID:9657673.
- Kral AM et al. (1997), J Biol Chem, 272, 27319-27323. Mutational analysis of conserved residues of the beta-subunit of human farnesyl:protein transferase. PMID:9341181.
- Fu HW et al. (1996), J Biol Chem, 271, 28541-28548. Identification of a cysteine residue essential for activity of protein farnesyltransferase. Cys299 is exposed only upon removal of zinc from the enzyme. PMID:8910483.
- Andres DA et al. (1993), J Biol Chem, 268, 1383-1390. Mutational analysis of alpha-subunit of protein farnesyltransferase. Evidence for a catalytic role. PMID:8419339.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Lys164A | electrostatic stabiliser |
| Tyr300B | electrostatic stabiliser |
| Asp297B | metal ligand |
| Cys299B | metal ligand |
| His362B | metal ligand |
| His248B | electrostatic stabiliser |
| Arg291B | electrostatic stabiliser |
| Lys294B | electrostatic stabiliser |
| Asp359B | electrostatic stabiliser |
| Asp352B | metal ligand |