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O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins
J E Hansen1, O Lund, K Rapacki
1Center for Biological Sequence Analysis, The Technical University of Denmark, Building 206, DK-2800 Lyngby, Denmark. janhan@cbs.dtu.dk
Nucleic Acids Research
|January 1, 1997
Summary
O-GLYCBASE is an updated glycoprotein database featuring O-linked glycosylation sites. This enhanced version includes more entries and detailed information on species, sequences, and glycan types for glycoproteins.
Area of Science:
- Biochemistry
- Bioinformatics
- Molecular Biology
Background:
- Glycoproteins play crucial roles in various biological processes.
- O-linked glycosylation is a significant post-translational modification affecting protein function.
- A centralized, updated database for O-linked glycosylation sites is essential for research.
Purpose of the Study:
- To present an updated version of the O-GLYCBASE database.
- To enhance the comprehensiveness and cross-referencing of O-linked glycosylation site information.
- To provide insights into acceptor specificity patterns of glycosyltransferases.
Main Methods:
- Compilation and revision of data from scientific literature and SWISS-PROT.
- Integration of cross-references to multiple biological databases (SWISS-PROT, PIR, PROSITE, PDB, EMBL, HSSP, LISTA, MIM).
- Generation of sequence logos to visualize enzyme specificity.
Main Results:
- The O-GLYCBASE database has been significantly expanded, with a 34% increase in entries since version 1.0.
- Detailed information on species, sequence, glycosylation sites, and glycan types is available.
- Sequence logos illustrating acceptor specificity for GalNAc, mannose, and GlcNAc transferases are presented.
Conclusions:
- O-GLYCBASE serves as a valuable, updated resource for O-linked glycosylation data.
- The database facilitates research by providing comprehensive and cross-referenced information.
- The inclusion of sequence logos aids in understanding glycosylation mechanisms.