O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins

Abstract

O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries with at least one experimentally verified O-glycosylation site have been compiled from protein sequence databases and literature. Each entry contains information about the glycan involved, the species, sequence, a literature reference and http-linked cross-references to other databases. Version 4.0 contains 179 protein entries, an approximate 15% increase over the last version. Sequence logos representing the acceptor specificity patterns for GalNAc, GlcNAc, mannosyl and xylosyl transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu.dk/databases/OGLYCBASE/

Identification and expression analysis of the human μ-protocadherin gene in fetal and adult kidneys

“…This mucin-type region structure is conserved between rat and human and contains a 31 amino acid motif that is repeated 3.5 times. As was experimentally observed with the rat -protocadherin ortholog (8), neural network predictions of mucin-type GalNAc Oglycosylation sites in human -protocadherin are that they are heavily glycosylated (data not shown) (23). In both the rat and the human forms, the mucin region is alternatively spliced to generate a protein with an extracellular region consisting of just the cadherin ectodomains.…”

“…The mucin domain was shown to be glycosylated in vivo in the rat kidney (8). On the basis of neural network predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins (23), the mucin region of the human -protocadherin gene is similarly predicted to be heavily glycosylated (data not shown). Conservation of the size and number of repeats within the mucin domain between the rat and human ortholog suggests the importance of the secondary structure of -protocadherin in its function.…”

Identification and functional characterisation of ctr1, a Pleurotus ostreatus gene coding for a copper transporter

“…An abundance of serine residues in the N-terminal region is also a feature of the copper transporter COPT1 from A. thaliana (Sanceno´n et al 2003) and substitution of the histidine residues by another polar amino acid such as serine could be the result of a conservative change that maintains the ability of the protein to interact with copper. A serine residue at position 15 in the P. ostreatus protein (that hypothetically corresponds to the outer N-terminal part of the protein) was predicted as a potential glycosylation site by the NetOGlyc server (Gupta et al 1999). Both the potential glycosylation site and the typical MLX 2 M motif conserved along copper transporters are found in the second transmembrane domain of the P. ostreatus Ctr1 protein.…”

Retracted: Prediction of posttranslational modification sites from sequences with kernel methods

“…23 We take out those proteins with annotations of mucin-type O-glycosylation linked to S or T in mammalian, excluding the proteins that have the annotation of "potential," "predicted," "similarity," or "probably." Finally, 255 proteins covered 842 mucin-type O-glycosylation S/T sites are obtained.…”