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Feb. 18, 2014:
OGTSite : a web server was constructed for identifying O-GlcNAcylation sites.

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- UniProtKB
  (Swiss-Prot)

- dbPTM v3
- dbOGAP
- O-GlycBase
- PhosphoSitePlus

Version: 1.0
(Feb. 18, 2014)


Welcome to OGTSite!

OGTSite is a web server for identifying O-GlcNAcylation sites. Protein O-GlcNAcylation, involving the β-attachment of single N-acetylglucosamine (GlcNAc) to the hydroxyl group of serine or threonine residues, is an O-linked glycosylation catalyzed by O-GlcNAc transferase (OGT). Molecular level investigation of the basis for OGT’s substrate specificity should aid understanding how O-GlcNAc contributes to diverse cellular processes. Due to the high-throughput of mass spectrometry (MS)-based proteomics, an increasing number of O-GlcNAcylated peptides with site-specific information were identified; as a result, several approaches have been proposed for the computational identification of O-GlcNAcylation sites. However, there exists no tool that identifies the O-GlcNAcylation sites with their corresponding OGT substrate motifs. Herein, we applied a recursively statistical method to obtain statistically significant conserved motifs from a large-scale dataset of O-GlcNAcylated sequences.

In this study, a non-redundant dataset of 410 experimentally verified O-GlcNAcylation sites were manually extracted from dbOGAP, OGlycBase and UniProtKB. After detection of conserved motifs on the 410 substrate sites, profile hidden Markov model (profile HMM) was adopted to learn a first-layered model for each identified OGT substrate motif. Support Vector Machine (SVM) was then used to generate a second-layered model learned from the output values of profile HMMs in first layer. The two-layered predictive model was evaluated using a five-fold cross validation which yielded a sensitivity of 85.4%, a specificity of 84.1%, and an accuracy of 84.7%. Additionally, an independent testing set from PhosphoSitePlus, which was really non-homologous to the training data of predictive model, was used to demonstrate that the proposed method could provide a promising accuracy (84.05%) and outperform other O-GlcNAcylation site prediction tools.

A case study demonstrated that the proposed method could be a feasible means of conducting preliminary analyses of protein O-GlcNAcylation and has been implemented as a web-based system, OGTSite, which is now freely available at http://csb.cse.yzu.edu.tw/OGTSite/.

  • Case Study 1 : KCC4_HUMAN, Calcium/calmodulin-dependent protein kinase type IV.
  • Case Study 2 : SYN1_RAT, Synapsin-1.
  • Investigation of O-GlcNAcylation sites

    Protein O-GlcNAcylation is an O-linked glycosylation involving the β-attachment of a single N-acetylglucosamine (GlcNAc) to the serine (Ser)/threonine (Thr) residues, adding 203.10 Da to the modified proteins. Two enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), are responsible for the addition and removal of O-GlcNAc, respectively. O-GlcNAcylation also happens reciprocal to phosphorylation at the same or adjacent Ser/Thr residues. To get a better understanding and characterize the potential linear consensus motif and adjacent amino acids surrounding to O-GlcNAcylated Ser/Thr residues, 375 experimentally verified Ser/Thr sites are further compared with the free Ser/Thr by two sample logo. The O-GlcNAcylation sites contain a higher preference of neutral residues (S, T, G. P, and V) than non- O-GlcNAcylation sites.




    Submission


  • Case Study 1 : KCC4_HUMAN, Calcium/calmodulin-dependent protein kinase type IV.
  • Case Study 2 : SYN1_RAT, Synapsin-1.