PDBsum entry: 1kzo

Transferase/transferase substrate

PDB id: 1kzo

Contents

Protein chains

323 a.a. *

407 a.a. *

Ligands

THR-LYS-CYS-VAL-ILE-MET

FPP

ACY

FAR

Metals

_ZN

Waters ×428

* Residue conservation analysis

PDB id:

1kzo

Name:

Transferase/transferase substrate

Title:

Protein farnesyltransferase complexed with farnesylated k-ra peptide product and farnesyl diphosphate substrate bound simultaneously

Structure:

Protein farnesyltransferase alpha subunit. Chain: a. Synonym: caax farnesyltransferase alpha subunit, ras protei prenyltransferase alpha, ftase-alpha. Engineered: yes. Protein farnesyltransferase beta subunit. Chain: b. Synonym: caax farnesyltransferase beta subunit, ras protein prenyltransferase beta, ftase-beta.

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_atcc_number: 63134. Synthetic: yes. Other_details: the peptide was chemically synthesized. The of the peptide is naturally found in homo sapiens.

Biol. unit:

Trimer (from PQS)

Resolution:

2.20Å R-factor: 0.159 R-free: 0.204

Authors:

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

Key ref:

S.B.Long et al. (2002). Reaction path of protein farnesyltransferase at atomic resolution. Nature, 419, 645-650. PubMed id: 12374986 DOI: 10.1038/nature00986

Date:

07-Feb-02 Release date: 16-Oct-02

Protein chain

Q04631  (FNTA_RAT) -  Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha

Seq: 377 a.a.

Struc: 323 a.a.

Protein chain

Q02293  (FNTB_RAT) -  Protein farnesyltransferase subunit beta

Seq: 437 a.a.

Struc: 407 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.5.1.58 - Protein farnesyltransferase.
• Reaction: Farnesyl diphosphate + protein-cysteine = S-farnesyl protein + diphosphate

Farnesyl diphosphate (Bound ligand (Het Group name = FPP) corresponds exactly) + protein-cysteine = S-farnesyl protein + diphosphate

• Cofactor: Magnesium; Zinc
• Enzyme class 2: Chain A: E.C.2.5.1.59 - Protein geranylgeranyltransferase type I.
• Reaction: Geranylgeranyl diphosphate + protein-cysteine = S-geranylgeranyl- protein + diphosphate

Geranylgeranyl diphosphate (Bound ligand (Het Group name = FPP) matches with 82.76% similarity) + protein-cysteine = S-geranylgeranyl- protein + diphosphate

• Cofactor: Zinc

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: protein complex (4 terms)
• Biological process: response to inorganic substance (15 terms)
• Biochemical function: catalytic activity (14 terms)

reference

DOI no: 10.1038/nature00986

Nature 419:645-650 (2002)

PubMed id: 12374986

Reaction path of protein farnesyltransferase at atomic resolution.

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

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% 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.

Selected figure(s)

Figure 2.
Figure 2: Comparison of reactant and product conformations and a proposed model for the transition state. a, Superposition of the observed structures of the substrates (blue) and the product (brown, isoprenoid; yellow, peptide) indicates reorganization of the isoprenoid upon product formation. The superposition was based on all FTase C[ ]atoms. b, Modelled transition state shown in stereo and in the same orientation as in a. The zinc ion activates the cysteine thiolate (green) for nucleophilic attack on the C[1] atom of the FPP substrate. Dashed lines indicate the scissile and nascent bonds. The C[1] atom has trigonal bipyramidal geometry; a triangle indicates that the C[1], C[2], H[1] and H[2] atoms lie in a plane. The FTase diphosphate ligands (grey coloured residues) are in conformations observed in complex 2. Residue Tyr 300 stabilizes the developing negative charge on the bridging oxygen between the -phosphate and the C[1] atom. Lys 164 and magnesium also stabilize negative charge on the phosphate.

Figure 3.
Figure 3: Farnesylated peptide product conformations at the active site (stereo). a, Product bound following catalysis (complex 3). The zinc ligands (grey) and those residues that have van der Waals contacts with the first or second isoprene units of the farnesyl moiety (C[1] to C[10]) are shown. Residues that interact with the third isoprene unit (C[11] to C[15]) are the same as in complexes with FPP7 and FPP analogues8,9. b, Product and FPP bound simultaneously (complex 4). Residues that interact with the farnesyl group of the product are shown. The two C-terminal amino acids of the product share the same conformation as observed in complexes 2 and 3. The C-terminal methionine side chain of this product has alternate conformations, labelled 'a' and 'b'. Conformation 'a' is the orientation observed in complexes 2 and 3.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2002, 419, 645-650) copyright 2002.

Figures were selected by the author.