PrePS - Prenylation Prediction Suite
Protein CaaX Farnesylation, CaaX Geranylgeranylation and Rab Geranylgeranylation

 


What is protein prenylation?

Prenylation refers to the posttranslational modification of proteins with isoprenyl anchors. These lipid moieties are typically involved in mediating protein-membrane but also protein-protein interactions of prominent cellular proteins. 3 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 C-termini of substrate proteins and attach farnesyl (15 carbon polyisopren) or geranylgeranyl (20 carbon polyisopren), respectively, to a required and spatially fixed cysteine in that motif. The third enzyme, geranylgeranyltransferase 2 (GGT2 or RabGGT) recognizes the complex 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 C-terminal motif.

Literature reviews:

Casey PJ, Seabra MC.
Protein prenyltransferases.
J Biol Chem. 1996 Mar 8;271(10):5289-92.

Sinensky M.
Recent advances in the study of prenylated proteins.
Biochim Biophys Acta. 2000 Apr 12;1484(2-3):93-106.

Roskoski R Jr.
Protein prenylation: a pivotal posttranslational process.
Biochem Biophys Res Commun. 2003 Mar 28;303(1):1-7.

Maurer-Stroh S, Washietl S, Eisenhaber F.
Protein prenyltransferases.
Genome Biol. 2003;4(4):212. Epub 2003 Apr 01.

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What is PrePS?

PrePS stands for Prenylation Prediction Suite and combines three predictors for protein CaaX farnesylation, CaaX geranylgeranylation and Rab geranylgeranylation in one webinterface. The predictors aim to model the substrate-enzyme interactions based on refinement of the recognition motifs for each of the prenyltransferases. Motif information has been extracted from sets of known substrates (learning sets) and specific scoring functions have been created utilizing both sequence as well as physical property profiles including interpositional correlations to account for partially overlapping substrate specificities. The PrePS selectively assigns the modifying enzyme to predicted substrate proteins and sensitively filters out false positive predictions based on the methodology that has already been applied successfully for the prediction of GPI-anchors, myristoylation and PTS1 peroxisomal targeting.

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How do I submit a sequence?

Simply copy/paste your sequence in the input form in single letter amino acid code or FASTA format.

Please only submit one sequence at a time and in case you want to run large-scale database predictions (e.g. for annotation purposes) you can contact us.

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What are the provided options?

You can select the prenylation of which of the three enzymes you want to be predicted.

The option for evOluation over NCBI's non-redundant database (NR) allows for evaluating the evolutionary motif conservation (evOluation). When selected, this option initiates a BLAST search for homologues in NR which takes, depending on our server load, between 0.5 and 2 minutes. Then, the BLAST hits are automatically submitted to PrePS and the prenylation prediction results annotated in the C-terminal alignment of the homologues.

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How do I interpret the results?

The two CaaX prenylation predictors (FT and GGT1) provide a score and estimation of the probability of false positive prediction, while the GGT2 predictor gives scores and E-values of the HMMer searches. Details of the profile and physical property terms of the scoring function or the HMMer alignments, respectively, are provided (follow link). Penalties on specific positions or regions can also be used to rationalize whether and why certain query sequences or artificial constructs (e.g. intended for membrane targeting) might be less suitable prenylation targets.

Please keep in mind that there are overlapping substrate specificities between the three prenyltransferases. As a simple rule, if a protein is a predicted GGT2 substrate then it often is geranylgeranylated by GGT2 in vivo also when it could be alternatively modified by FT or GGT1 in vitro (as would be indicated by a prediction as FT or GGT1 substrate). In the case of predicted substrates for both FT and GGT1, our method was found to correlate best with experimentally verified enzyme affinities when comparing the relative scores of the predictors with the GGT1 score divided by 3 (because GGT1 seems to have a 3-fold lower activity compared to FT). Proteins ending with a -CxxL motif were previously thought to be classical GGT1 substrates but can also be alternatively modified to a certain extent by FT in vitro due to its broad substrate specificity. In vivo, however, these proteins ending with a leucine are likely to be geranylgeranylated by GGT1.

PrePS gives additional quality assignments for better comparison of the individual predictions. These are, with decreasing likelihood of being a prenylation target: +++, ++, +, -, -- and ---. The different PLUS attributes describe the quality of proteins as PREDICTED prenylation substrates. A MINUS attribute means that the query sequence is NOT PREDICTED to be prenylated with distinction on how far the query has been from the prediction limit.

In case the evOluation option was used, the evolutionary motif conservation can be evaluated from the alignment of the C-termini of homologous sequences in combination with the respective PrePS predictions. For example, a prenylation motif that is conserved in a series of homologues in different organisms might be biologically more important than an isolated prediction.

IMPORTANT: Please note that PrePS only can tell you whether a protein would be processed by the prenylating enzymes when provided as substrate. This prediction does not necessarily imply a cellular context for the query protein that would allow in vivo access to the respective enzymes.

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How do I cite PrePS?

The manuscript describing PrePS is available from the Genome Biology website (http://genomebiology.com/2005/6/6/R55) and can be cited as:

Maurer-Stroh S, Eisenhaber F
Refinement and prediction of protein prenylation motifs
Genome Biology 2005, 6:R55 doi:10.1186/gb-2005-6-6-r55

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For more questions or comments, please contact Sebastian