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

Long, Stephen B.; Hancock, Paula J.; Kral, Astrid M.; Hellinga, Homme W.; Beese, L.S.

doi:10.1073/pnas.241407898

Cited by 112 publications

(189 citation statements)

References 35 publications

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“…Structure of Active Ternary Complex-The crystal structures of FTase and GGTase I indicate that the substrates bound in their respective ternary and product complexes have a similar overall conformation (12,50,52). The first three isoprene units of 3-aza-GGPP are arranged along a straight line in the central cavity of the ␤-subunit of GGTase I, with the first isoprene unit shifted 1 Å relative to the crystal structure of an FPP analog bound to FTase (12).…”

Section: Discussionmentioning

confidence: 99%

Lysine β311 of Protein Geranylgeranyltransferase Type I Partially Replaces Magnesium

Hartman

Bowers

Fierke

2004

Journal of Biological Chemistry

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Protein geranylgeranyltransferase type I (GGTase I) catalyzes the attachment of a geranylgeranyl lipid group near the carboxyl terminus of protein substrates. Unlike protein farnesyltransferase (FTase) and protein geranylgeranyltransferase type II, which require both Zn(II) and Mg(II) for maximal turnover, GGTase I turnover is dependent only on Zn(II). In FTase, the magnesium ion is coordinated by aspartate ␤352 and the diphosphate of farnesyl diphosphate to stabilize the developing charge in the transition state (Pickett, J. S., Bowers, K. E., and Fierke, C. A. Prenylation is a type of post-translational modification where a lipid group from either farnesyl diphosphate (FPP) 1 or geranylgeranyl diphosphate (GGPP) is covalently attached via a thioether linkage to a conserved cysteine residue near the carboxyl terminus of a protein (1-6; for review, see Refs. 7 and 8). The attached lipid mediates membrane association and specific protein-protein interactions, which are obligatory for proper functioning of the modified protein (9, 10). Protein farnesyltransferase (FTase), protein geranylgeranyltransferase type I (GGTase I), and protein geranylgeranyltransferase type II (GGTase II) comprise the class of zinc-catalyzed sulfur alkylation enzymes known as the protein prenyltransferases.All three protein prenyltransferases are ␣/␤ heterodimers; FTase and GGTase I share common ␣-subunits and possess ␤-subunits with 25% sequence identity (8,11,12). FTase and GGTase I prenylate proteins or peptides containing carboxylterminal CaaX (C refers to a conserved cysteine residue, a refers to an aliphatic amino acid, and X generally refers to leucine or phenylalanine for GGTase I, and methionine, serine, alanine, or glutamine for FTase) sequences (13-18). The proteins Ras, RhoB, CENP-E, and CENP-F are known substrates of FTase; GGTase I modifies the ␥-subunits of most heterotrimeric G proteins as well as many Ras-related G proteins, including members of the Rac, Rap, and Rho families (9, 19 -23). In a fashion distinct from FTase and GGTase I, GGTase II catalyzes the attachment of two geranylgeranyl groups to members of the Rab family of GTPases that contain carboxylterminal sequences of XXCC, XCXC, XCCX, and CCXX (C refers to a conserved cysteine residue, and X refers to any amino acid) (24).Recently, much of the work on prenyltransferases has focused on FTase and the protein substrate, Ras, a small GTPase in the receptor tyrosine kinase signaling pathway that is a key regulator of cell division (25). 30% of all human cancers can be linked to mutations in the ras gene, which lead to constitutively activated Ras signaling (25). The post-translational attachment of a farnesyl group by FTase is required for the transforming activity of Ras oncoproteins (25). These observations prompted a search for FTase inhibitors as novel anticancer agents (25). Subsequent research demonstrated that the form of Ras most often mutated in human cancers is K-Ras4B, a protein substrate that can be farnesylated by FTase as well as geranylgeranylated by...

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Section: Discussionmentioning

confidence: 99%

Lysine β311 of Protein Geranylgeranyltransferase Type I Partially Replaces Magnesium

Hartman

Bowers

Fierke

2004

Journal of Biological Chemistry

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“…1) (26,28,35). An x-ray crystal structure of the FTase⅐product complex and mutagenesis studies of the diphosphate binding pocket suggest that an active structure may by achieved by a conformational change of FPP in which the first two prenyl groups rotate (37,38).…”

mentioning

confidence: 99%

Mutagenesis Studies of Protein Farnesyltransferase Implicate Aspartate β352 as a Magnesium Ligand

Pickett

Bowers

Fierke

2003

Journal of Biological Chemistry

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Protein farnesyltransferase (FTase) 1 catalyzes the transfer of a 15-carbon farnesyl chain from farnesyl diphosphate (FPP) to a C-terminal cysteine sulfur of protein substrates in the cell (1). Protein or peptide substrates of FTase contain a C-terminal CaaX sequence, whereas C represents the cysteine that becomes farnesylated, a 1 and a 2 are typically small aliphatic amino acids, and X is commonly methionine, serine, glutamine, or alanine (2). FTase is known to modify several important proteins in the cell cycle machinery, including Ras, Rho B, CENP-E, and CENP-F (3). Farnesylation of proteins enhances membrane association and specific protein-protein interactions and therefore is thought to be important for localization of proteins in the cell (4 -6). After farnesylation by FTase, proteins are further processed by the CaaX protease Rce1 and the methyltransferase Icmt, producing a Cterminal farnesylated cysteine methyl ester as the end product of this pathway (7,8). Protein farnesyltransferase inhibitors are currently being evaluated in clinical trials for the treatment of several types of cancer, including acute myeloid leukemia, metastatic breast cancer, and non-small cell lung cancer (9, 10).Farnesylation is just one type of protein prenylation; proteins can also be modified with geranylgeranyl groups in a reaction catalyzed by geranylgeranyl transferase type I or type II (GGTase I and GGTase II) (11, 12). GGTase I also recognizes protein substrates with a C-terminal CaaX motif, but GGTase I substrates most frequently contain a leucine or phenylalanine at the X position (13, 14). FTase and GGTase I are structurally homologous heterodimers with identical ␣ subunits and differing ␤ subunits (15). Prenyltransferases contain an active site zinc ion that is required for activity; FTase and GGTase II also use a magnesium ion to facilitate catalysis (16 -19). Surprisingly, GGTase I apparently catalyzes the same prenyl transfer reaction with no dependence on magnesium ions (20).In FTase, the magnesium ion has been proposed to coordinate to the diphosphate of FPP, but the exact location of the magnesium binding site has not yet been identified (21). The bound zinc ion of FTase coordinates to the cysteine sulfur of the protein substrate, lowering the pK a to form a zincthiolate at neutral pH (22, 23). In the proposed farnesylation transition state of FTase (Scheme 1), positive charge accumulates on the C-1 of FPP, and the diphosphate leaving group develops additional negative charge (24, 25). Bound magnesium is proposed to stabilize the negative charge buildup on the diphosphate moiety and activate the leaving group (21). Although magnesium is not absolutely required for FTase catalysis, millimolar concentrations of magnesium ions enhance the rate constant for product formation by 700-fold (24).Several pieces of experimental evidence indicate that the diphosphate of FPP forms part of the magnesium binding site. X-ray crystallography of the FTase ternary complex in the presence of manganese showed a manganese ion bo...

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“…A set of parameters specifically designed to allow a reliable treatment of the Zn 2+ coordination sphere formed during catalysis and based on DFT (B3LYP) and molecular mechanical calculations 31 , crystallographic data [32][33][34] , extended X-ray absorption fine structure (EXAFS) results 35 and on several other more recent mechanistic studies 36,37 were applied to the systems in study. These parameters are described in detail elsewhere 38 and have been already used with success in the study of FTase [38][39][40] .…”

Section: Simulationsmentioning

confidence: 99%

Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery

Moorthy

Sousa

Ramos

et al. 2016

Journal of Enzyme Inhibition and Medicinal Chemistry

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Farnesyltransferase is one of the enzyme targets for the development of drugs for diseases, including cancer, malaria, progeria, etc. In the present study, the structure-based pharmacophore models have been developed from five complex structures (1LD7, 1NI1, 2IEJ, 2ZIR and 2ZIS) obtained from the protein data bank. Initially, molecular dynamic (MD) simulations were performed for the complexes for 10 ns using AMBER 12 software. The conformers of the complexes (75) generated from the equilibrated protein were undergone protein-ligand interaction fingerprint (PLIF) analysis. The results showed that some important residues, such as LeuB96, TrpB102, TrpB106, ArgB202, TyrB300, AspB359 and TyrB361, are predominantly present in most of the complexes for interactions. These residues form side chain acceptor and surface (hydrophobic or -) kind of interactions with the ligands present in the complexes. The structure-based pharmacophore models were generated from the fingerprint bits obtained from PLIF analysis. The pharmacophore models have 3-4 pharmacophore contours consist of acceptor and metal ligation (Acc & ML), hydrophobic (HydA) and extended acceptor (Acc2) features with the radius ranging between 1-3 Å for Acc & ML and 1-2 Å for HydA. The excluded volumes of the pharmacophore contours radius are between 1-2 Å . Further, the distance between the interacting groups, root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radial distribution function (RDF) analysis were performed for the MDsimulated proteins using PTRAJ module. The generated pharmacophore models were used to screen a set of natural compounds and database compounds to select significant HITs. We conclude that the developed pharmacophore model can be a significant model for the identification of HITs as FTase inhibitors.

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

Cited by 112 publications

References 35 publications

Lysine β311 of Protein Geranylgeranyltransferase Type I Partially Replaces Magnesium

Lysine β311 of Protein Geranylgeranyltransferase Type I Partially Replaces Magnesium

Mutagenesis Studies of Protein Farnesyltransferase Implicate Aspartate β352 as a Magnesium Ligand

Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery

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