IMP GPI Lipid Anchor Project IMP-Bioinformatics

Sequence analysis of GPI-anchored proteins on the proprotein level

Contact:
Birgit Eisenhaber (MDC/IMP)
Peer Bork (MDC/EMBL)
Frank Eisenhaber (IMP)

Eisenhaber B., Bork P., Eisenhaber F.
"Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase"
Protein Engineering (1998) 11, No.12, 1155-1161

Glycosylphosphatidylinositol (GPI) anchoring is a common posttranslational modification of extracellular eukariotic proteins. Attachment of the GPI moiety to the carboxyl terminus (omega-site) of the polypeptide occurs after proteolytic cleavage of a C-terminal propeptide. In this work, the sequence pattern for GPI-modification has been 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 (omega-11)...(omega-1) and (omega+4)...(omega+5). We present statistical evidence for volume-compensating residue exchanges with respect to the positions (omega-1)...(omega-2). Differences between protozoan and metazoan GPI-modification motifs consist mainly in variations of preferences to amino acid types at the positions near the omega-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 (omega-1)...(omega+2) appears about 540 ų.

List of 155 SWISS-PROT entries with annotated GPI-site
amino acid property library

Correlation data with amino acid properties
ProtozoaMetazoa
1) for alignment of largest subset 1) for alignment of largest subset
2) for effective amino acid composition of total alignment 2) for effective amino acid composition of total alignment



Length distribution of GPI-anchor propeptides


Model of the polypeptide binding site of the putative transamidase complex


Last modified: 11th June 2002