UbiProt: a database of ubiquitylated proteins - PubMed (original) (raw)

UbiProt: a database of ubiquitylated proteins

Alexander L Chernorudskiy et al. BMC Bioinformatics. 2007.

Abstract

Background: Post-translational protein modification with ubiquitin, or ubiquitylation, is one of the hottest topics in a modern biology due to a dramatic impact on diverse metabolic pathways and involvement in pathogenesis of severe human diseases. A great number of eukaryotic proteins was found to be ubiquitylated. However, data about particular ubiquitylated proteins are rather disembodied.

Description: To fill a general need for collecting and systematizing experimental data concerning ubiquitylation we have developed a new resource, UbiProt Database, a knowledge base of ubiquitylated proteins. The database contains retrievable information about overall characteristics of a particular protein, ubiquitylation features, related ubiquitylation and de-ubiquitylation machinery and literature references reflecting experimental evidence of ubiquitylation. UbiProt is available at http://ubiprot.org.ru for free.

Conclusion: UbiProt Database is a public resource offering comprehensive information on ubiquitylated proteins. The resource can serve as a general reference source both for researchers in ubiquitin field and those who deal with particular ubiquitylated proteins which are of their interest. Further development of the UbiProt Database is expected to be of common interest for research groups involved in studies of the ubiquitin system.

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Figures

Figure 1

Figure 1

Structure of a typical UbiProt entry. This entry contains information about an ubiquitylated NEMO protein.

Figure 2

Figure 2

Different forms of ubiquitin and ubiquitin-modified proteins. Ubiquitylation may result in addition of a single ubiquitin moiety or a branched multi-ubiquitin chain to the target protein lysine(s). Note that a ubiquitin molecule possesses 7 inner lysine residues that can serve as attachment sites of the next ubiquitin moiety, resulting in the formation of the chains that have a different structure and topology. Functionally significant amino acids are marked as follows: Kn and Kn' – lysine residue(s) that can serve as attachment sites of the ubiquitin moiety; G76 – ubiquitin C-terminal glycine residue participating in the isopeptide bond formation. Poly-ubiquitin refers to a ubiquitin fusion protein, a precursor form polymerized "head-to-tail".

Figure 3

Figure 3

Example of full-text search results. The search pattern is "ubch5*" that corresponds to the particular E2 ubiquitin-conjugation enzyme (UbcH5). The result shows proteins to be modified by the specified enzyme.

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