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Glycobiology Advance Access published online on September 26, 2003
Glycobiology, doi:10.1093/glycob/cwh004
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Submitted on June 10, 2003
Revised on August 8, 2003
Accepted on September 3, 2003

© 2003 Oxford University Press

ORIGINAL ARTICLES

Biases and complex patterns in the residues flanking protein N-glycosylation sites

Shifra Ben-Dor 1, Nir Esterman 2, Eitan Rubin 1, and Nathan Sharon 2*

1 Department of Biological Services, The Weizmann Institute of Science, Rehovot, 76100, Israel
2 Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100, Israel

* To whom correspondence should be addressed. E-mail: Nathan.Sharon{at}weizmann.weizmann.ac.il.

Abstract

N-Glycosylation, the most common and most versatile protein modification reaction, occurs at the {beta}-amide of the aspargine of the Asn-Xaa-Ser/Thr sequon. For reasons that are unclear, not all such sequons are glycosylated. To find patterns that affect glycosylation we examined the amino acid residues from the twentieth preceding the sequon to the twentieth residue following it, utilizing bioinformatics tools. A clean dataset of annotated, experimentally verified, glycosylated and non-glycosylated sequons derived from 617 well-defined non-redundant N- and N-,O-glycoproteins listed in SWISS-PROT (June 2002) was used. NXS and NXT sequons were analyzed separately. Although no overt patterns were found to explain sequon occupancy or non-occupancy, trends for over- or under-representation of certain amino acids at particular positions were statistically significant, and different in NXS and NXT sequons. In extension of earlier reports, none of the 80 Asn-Pro-Ser/Thr found were glycosylated and a markedly low level of glycosylation was seen in sequons with Pro at the position following the Ser/Thr. In addition, a general observation was made that the considerable number of glycosylated sequons in the C-terminal 10 residues of glycoproteins suggesting that N-glycosylation in these cases may be post-translational and not co-translational, as widely accepted.


bioinformatics, database survey, glycoproteins, glycosylation frequency, sequon
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