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Bioinformatics Advance Access originally published online on July 15, 2004
Bioinformatics 2004 20(18):3302-3307; doi:10.1093/bioinformatics/bth407
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Discovery Note

Preferred in vivo ubiquitination sites

André Catic 1,*, Cal Collins 2, George M. Church 3 and Hidde L. Ploegh 1

1 Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA, 2 Akaza Research, Inc., 56 John F. Kennedy Street, Cambridge, MA 02138, USA and 3 Lipper Center for Computational Genetics and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA

Received on April 6, 2004; revised on June 20, 2004; accepted on July 7, 2004
Advance Access Publication July 15, 2004

Motivation: The conjugation of ubiquitin to target molecules involves several enzymatic steps. Little is known about the specificity of ubiquitination. How E3 ligases select their substrate and which lysines are targeted for ubiquitin conjugation is largely an enigma. The object of this study is to identify preferred ubiquitination sites. Genetic approaches to study this question have proven difficult, because of the redundancy of ligases and the lack of strictly required motifs. However, a better understanding of acceptor site selection could help to predict ubiquitination sites and clarify yet unsolved structure–function relationships of the transfer reaction.

Results: In an effort to define preferences for ubiquitination, we systematically analyzed structure and sequence of 135 known ubiquitination sites in 95 proteins in Saccharomyces cerevisiae. The results show clear structural preferences for ubiquitin ligation to target proteins, and compartment-specific amino acid patterns in close proximity to the modified side chain.

Supplementary information: http://www.people.fas.harvard.edu/~catic

Contact: Catic{at}fas.harvard.edu

* To whom correspondence should be addressed.


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