Sequence properties of GPI-anchored proteins near the ω-site: Constraints for the polypeptide binding site of the putative transamidase

Abstract

Glycosylphosphatidylinositol (GPI) anchoring is a common post-translational modification of extracellular eukaryotic proteins. Attachment of the GPI moiety to the carboxyl terminus to-site) of the polypeptide occurs after proteolytic cleavage of a C-terminal propeptide. In this work, the sequence pattern for GPI-modification was analyzed in terms of physical amino acid properties based on a database analysis of annotated proprotein sequences. In addition to a refinement of previously described sequence signals, we report conserved sequence properties in the regions ω - 11...ω - 1 and ω + 4...ω + 5. We present statistical evidence for volume-compensating residue exchanges with respect to the positions ω - 1...ω + 2. Differences between protozoan and metazoan GPI-modification motifs consist mainly in variations of preferences to amino acid types at the positions near the ω-site and in the overall motif length. The variations of polypeptide substrates are exploited to suggest a model of the polypeptide binding site of the putative transamidase, the enzyme catalyzing the GPI-modification. The volume of the active site cleft accommodating the four residues ω - 1...ω + 2 appears to be ~ 540 Å3.