Abstract
BackgroundUbiquitination is an important post-translational modification involved in diverse biological processes. Therefore, genomewide representation of the ubiquitination system for a species is important.DescriptionSCUD is a web-based database for the ubiquitination system in Saccharomyces cerevisiae (Baker's yeast). We first searched for all the known enzymes involved in the ubiquitination process in yeast, including E1, E2, E3, and deubiquitination enzymes. Then, ubiquitinated substrates were collected by literature search. Especially, E3 and deubiquitination enzymes are classified into classes and subclasses by their shared domains and unique functions. As a result, 42 different E3 enzymes were grouped into corresponding classes and subclasses, and 940 ubiquitinated substrates including mutant substrates were identified. All the enzyme and substrate information are interconnected by hyperlinks, which makes it easy to view the enzyme-specific ubiquitination information.ConclusionThis database aims to represent a comprehensive yeast ubiquitination system, and is easily expandable with the further experimental data. We expect that this database will be useful for the research on the ubiquitination systems of other higher organisms.SCUD is accessible at
Highlights
Ubiquitination is an important post-translational modification involved in diverse biological processes
This database aims to represent a comprehensive yeast ubiquitination system, and is expandable with the further experimental data. We expect that this database will be useful for the research on the ubiquitination systems of other higher organisms
For E3 enzymes, we looked for all the proteins showing ubiquitin-protein ligase activity and extracted the proteins involved in substrate recognition independently or dependently on other proteins
Summary
Ubiquitination is involved in many biological processes including cell signaling pathway and protein quality checkpoint system, by which ubiquitinated proteins are delivered to the 26S proteasome and degraded. Ubiquitinated site information would help identify the conditions on which specific lysines are selected and ubiquitinated For these purposes, we searched for all the known enzymes involved in the ubiquitination process in budding yeast, Saccharomyces cerevisiae, and classified E3 enzymes into E3 classes and subclasses. For E3 enzymes, we looked for all the proteins showing ubiquitin-protein ligase activity and extracted the proteins involved in substrate recognition independently or dependently on other proteins (in case of complexes). Identification of Ubiquitinated Substrates Using each substrate receptor in each E3 enzyme class or subclass as a query, we collected by literature search all substrate information as well as E2 and deubiquitination
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