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Abstract

Refinement and prediction of protein prenylation motifs <p>Three prenylation motif predictions are presented that allow discrimination between proteins that are unique substrates of farnesyltransferase (FT) and those that can be alternatively processed by geranylgeranyltransferase I (GGT1).</p> AbstractWe refined the motifs for carboxy-terminal protein prenylation by analysis of known substrates for farnesyltransferase (FT), geranylgeranyltransferase I (GGT1) and geranylgeranyltransferase II (GGT2). In addition to the CaaX box for the first two enzymes, we identify a preceding linker region that appears constrained in physicochemical properties, requiring small or flexible, preferably hydrophilic, amino acids. Predictors were constructed on the basis of sequence and physical property profiles, including interpositional correlations, and are available as the Prenylation Prediction Suite (PrePS, http://mendel.imp.univie.ac.at/sat/PrePS) which also allows evaluation of evolutionary motif conservation. PrePS can predict partially overlapping substrate specificities, which is of medical importance in the case of understanding cellular action of FT inhibitors as anticancer and anti-parasite agents. RationalePrenylation refers to the posttranslational modification of proteins with isoprenyl anchors [1][2][3]. These lipid moieties are typically involved in mediating not only protein-membrane but also protein-protein interactions. Three eukaryotic enzymes are known to catalyze the lipid transfer. The first two, farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1), recognize the so-called CaaX box in the carboxy termini of substrate proteins and attach farnesyl (15-carbon polyisoprene) or geranylgeranyl (20-carbon polyisoprene), respectively, to a required and spatially fixed cysteine in that motif. The third enzyme, geranylgeranyltransferase 2 (GGT2 or RabGGT) recognizes the complex [4] of Rab GTPase substrate proteins with a specific Rab escort protein (REP) to attach one or two geranylgeranyl anchors to cysteines in a more flexible but also carboxy-terminal motif.The CaaX box was initially understood to consist of a cysteine (C), followed by two aliphatic residues (aa) and a terminal residue (X) that would direct modification by either FT or GGT1, but newly found substrates and kinetic studies of mutated substrate peptides and enzyme inhibitors have shown that the motif recognized by the enzymes appears to be more flexible [2]. Furthermore, the determination of preference for FT or GGT1 is more complex and a function of the overall sequence context rather than specific amino acids at single positions. Whereas GGT2 appears to be specific to Rab GTPases as substrates, the recognition mechanism is not well understood. Overlapping substrate specificities between all three prenylating enzymes further complicate the understanding of the lipid modification process [5,6].An unsolved problem so far is accounting for the complexity of the prenylation substrate recognition motifs in theoretical models in order to ident...

N-Myristoylation Regulates the SnRK1 Pathway inArabidopsis

“…Gordon and colleagues (reviewed in Bhatnagar et al, 2001). Our data are entirely consistent with published results (Maurer-Stroh et al, 2002a, 2002b. The main difference between Sc NMT and At NMT1 is the more restricted substrate specificity of Sc NMT due to the inability of this enzyme to acylate protein substrates with acidic residues at both positions 8 and 9.…”

“…Higher eukaryotes often have two NMTs. There are therefore five classes of NMTs (one in protists, two in plants, and two in animals), reflecting variations in substrate specificity (see Maurer-Stroh et al, 2002b, 2002a. We hypothesized that complementation of the nmt1-1 knockout with NMTs from each of the five classes could be used to identify the protein subsets involved in each of the defects displayed by this mutant in early development and fruit and flower development.…”

“…Recognition is based on the chemical properties of the first eight residues of the peptide sequence, with only the nature of the first residue (Gly) strictly defined and fixed. Moreover, several studies have indicated that orthologous NMTs have overlapping but different substrate specificities (Towler et al, 1988;Maurer-Stroh et al, 2002a. For instance, a higher eukaryotic NMT has been shown to acylate several substrates in vitro that the Saccharomyces cerevisiae NMT is unable to modify .…”

ORF7 of Varicella-Zoster Virus Is a Neurotropic Factor

“…The gene is 780 bp long with a predicted size of 29 kDa (14). Bioinformatic analysis of VZV ORF7 resulted in the following predictions: (a) globular protein with a structured N terminus consisting of random coil/alphahelix-rich regions interspaced by extended sheets and a flexible, disordered proline-rich C terminus (12,35); (b) globular, soluble protein with no predicted transmembrane motifs (18,28,38); (c) four predicted phosphorylation sites but none conserved in the other human alphaherpesviruses or in PrV-1, suggesting a potentially different pattern or functional significance of ORF7 phosphorylation, if it indeed occurs (6, 7); (d) conserved cysteine at position 9, possible palmitoylation site (47) but no predicted myristoylation or prenylation (farnesyl/geranyl) sites (39). The HSV homolog UL51 is a tegument phosphoprotein associated with the trans-Golgi network (TGN) and whose deletion caused a decrease in titer and in plaque size (13,42,43).…”

C35 (C17orf37) is a novel tumor biomarker abundantly expressed in breast cancer

“…A prenylation site is predicted with a high degree of certainty at the COOH terminus. Prenylation promotes membrane association by attachment of hydrophobic moiety, thereby producing a protein with a substantially higher affinity for the membrane (18,31). Other proteins that contain prenylation sites include the Ras oncogene family, whose function in signal transduction cascades and transforming potential are dependent on prenylation-induced translocation to the membrane (32,33).…”