Refinement and prediction of protein prenylation motifs

Genome Biol. 2005;6(6):R55. doi: 10.1186/gb-2005-6-6-r55. Epub 2005 May 27.


We 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, 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alkyl and Aryl Transferases / chemistry
  • Amino Acid Motifs*
  • Amino Acid Sequence
  • Animals
  • Computational Biology / methods*
  • Conserved Sequence
  • Evolution, Molecular
  • Humans
  • Internet
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Prenylation*
  • Reproducibility of Results
  • Sequence Alignment
  • Software
  • Substrate Specificity


  • Alkyl and Aryl Transferases
  • geranylgeranyltransferase type-I
  • p21(ras) farnesyl-protein transferase