PDBsum entry 1jcs

Transferase/transferase inhibitor

PDB id: 1jcs

Contents

Protein chains

323 a.a. *

407 a.a. *

Ligands

THR-LYS-CYS-VAL-PHE-MET

FII

ACY ×2

Metals

_ZN

Waters ×436

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The crystal structure of human protein farnesyltransferase reveals the basis for inhibition by caax tetrapeptides and their mimetics.

Authors

S.B.Long, P.J.Hancock, A.M.Kral, H.W.Hellinga, L.S.Beese.

Ref.

Proc Natl Acad Sci U S A, 2001, 98, 12948-12953. [DOI no: 10.1073/pnas.241407898]

PubMed id

11687658

Abstract

Protein farnesyltransferase (FTase) catalyzes the attachment of a farnesyl lipid group to the cysteine residue located in the C-terminal tetrapeptide of many essential signal transduction proteins, including members of the Ras superfamily. Farnesylation is essential both for normal functioning of these proteins, and for the transforming activity of oncogenic mutants. Consequently FTase is an important target for anti-cancer therapeutics. Several FTase inhibitors are currently undergoing clinical trials for cancer treatment. Here, we present the crystal structure of human FTase, as well as ternary complexes with the TKCVFM hexapeptide substrate, CVFM non-substrate tetrapeptide, and L-739,750 peptidomimetic with either farnesyl diphosphate (FPP), or a nonreactive analogue. These structures reveal the structural mechanism of FTase inhibition. Some CaaX tetrapeptide inhibitors are not farnesylated, and are more effective inhibitors than farnesylated CaaX tetrapeptides. CVFM and L-739,750 are not farnesylated, because these inhibitors bind in a conformation that is distinct from the TKCVFM hexapeptide substrate. This non-substrate binding mode is stabilized by an ion pair between the peptide N terminus and the alpha-phosphate of the FPP substrate. Conformational mapping calculations reveal the basis for the sequence specificity in the third position of the CaaX motif that determines whether a tetrapeptide is a substrate or non-substrate. The presence of beta-branched amino acids in this position prevents formation of the non-substrate conformation; all other aliphatic amino acids in this position are predicted to form the non-substrate conformation, provided their N terminus is available to bind to the FPP alpha-phosphate. These results may facilitate further development of FTase inhibitors.

Figure 1.
Fig. 1. Chemical structures.

Figure 2.
Fig. 2. Structure of human FTase in complex with the CIFM-derived L-739,750 peptidomimetic and FPP substrate. (A) Overall structure. (B) 6 F[O]-F[C] omit electron density for L-739,750. The FPP substrate and zinc ion are included for reference. (C) Residues forming van der Waals interactions with L-739,750, shown in stereo. The N terminus of the peptidomimetic forms an ion pair with an -phosphate oxygen of the FPP substrate.

Secondary reference #1

Title

The basis for k-Ras4b binding specificity to protein farnesyltransferase revealed by 2 a resolution ternary complex structures.

Authors

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

Ref.

Structure, 2000, 8, 209-222. [DOI no: 10.1016/S0969-2126(00)00096-4]

PubMed id

10673434

Figure 6.
Figure 6. b-Turn conformation of the Ca[1]a[2]X box of the peptide (yellow) bound to zinc-depleted FTase. The zinc-coordinated conformation (light blue) is superimposed. This view is approximately the same as that shown in Figure 4.

The above figure is reproduced from the cited reference with permission from Cell Press

Secondary reference #2

Title

Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution.

Authors

H.W.Park, S.R.Boduluri, J.F.Moomaw, P.J.Casey, L.S.Beese.

Ref.

Science, 1997, 275, 1800-1804. [DOI no: 10.1126/science.275.5307.1800]

PubMed id

9065406

Figure 2.
Fig. 2. The subunit. (A) Aromatic pocket in the center of the - barrel of the subunit. This view is a 90° clockwise^ rotation relative to Fig. 1A. Only helices 2 to 13 are shown. Yellow, the nine aromatic residues that line the pocket; magenta, the zinc ion [MOLSCRIPT (40) and RASTER3D (41)]. (B) A portion of the solvent-accessible surface showing some of the^ aromatic residues that line the putative FPP binding pocket. FPP is modeled with the isoprenoid in the hydrophobic cleft and the^ diphosphate moiety positioned near the zinc. The carbon atoms of FPP are yellow, oxygens are red, and phosphates are green. The program INSIGHT II (43) was used to construct an energy-minimized^ model of FPP and GRASP (44) was used to calculate the accessible^ surface.

Figure 3.
Fig. 3. (A) Solvent-accessible surface and electrostatic surface potential. The dashed box highlights the cleft where the^ nonapeptide binds. The most negative electrostatic surface potential (-10 kT) is colored red. The most positive electrostatic surface^ potential (10 kT) is blue. The orientation is similar to that of Fig. 1. The arrow indicates the putative FPP binding site [GRASP (44)]. (B) Close-up view of the nonapeptide binding cleft bounded by the dashed lines in (A). The COOH-terminus and six residues of the nonapeptide (Ala^9-Val8-Thr7-Ser6-Asp5-Pro4) are visible. Atom colors for the nonapeptide are coral, carbons; red, oxygen; light blue, nitrogen; and zinc, magenta. (C) Stereo view of the nonapeptide (COOH-terminus of a symmetry-related^ subunit). The nonapeptide is numbered from the COOH-terminus. Atom colors in the nonapeptide are coral, carbons; orange, oxygen; and light blue, nitrogen. Atom colors of residues forming the^ binding pocket are khaki, carbons; red, oxygen; and blue, nitrogen. Zinc is a magenta sphere. Water molecules are red spheres. Dotted^ lines represent potential hydrogen bonds.

The above figures are reproduced from the cited reference with permission from the AAAs