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Open Access Highly Accessed Database

SCUD: Saccharomyces Cerevisiae Ubiquitination Database

Won-Chul Lee12, Minho Lee1, Jin Woo Jung2, Kwang Pyo Kim23* and Dongsup Kim1*

Author Affiliations

1 Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea

2 Department of Molecular Biotechnology, Konkuk University, Seoul 143-701, Korea

3 Institute of Biomedical Science and Technology, Konkuk University, Seoul 143-701, Korea

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BMC Genomics 2008, 9:440  doi:10.1186/1471-2164-9-440

Published: 24 September 2008

Abstract

Background

Ubiquitination is an important post-translational modification involved in diverse biological processes. Therefore, genomewide representation of the ubiquitination system for a species is important.

Description

SCUD 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.

Conclusion

This 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 http://scud.kaist.ac.kr webcite