Abstract
MotivationProtein ubiquitination is one of the important post-translational modifications by attaching ubiquitin to specific lysine (K) residues in target proteins, and plays important regulatory roles in many cell processes. Recent studies indicated that abnormal protein ubiquitination have been implicated in many diseases by degradation of many key regulatory proteins including tumor suppressor, oncoprotein, and cell cycle regulator. The detailed information of protein ubiquitination sites is useful for scientists to investigate the mechanism of many cell activities and related diseases.ResultsIn this study we established mUbiSida for mammalian Ubiquitination Site Database, which provides a scientific community with a comprehensive, freely and high-quality accessible resource of mammalian protein ubiquitination sites. In mUbiSida, we deposited about 35,494 experimentally validated ubiquitinated proteins with 110,976 ubiquitination sites from five species. The mUbiSiDa can also provide blast function to predict novel protein ubiquitination sites in other species by blast the query sequence in the deposit sequences in mUbiSiDa. The mUbiSiDa was designed to be a widely used tool for biologists and biomedical researchers with a user-friendly interface, and facilitate the further research of protein ubiquitination, biological networks and functional proteomics. The mUbiSiDa database is freely available at http://reprod.njmu.edu.cn/mUbiSiDa.
Highlights
Protein ubiquitination, known as the important protein posttranslational modification of targeting proteins by ubiquitins for their subsequent degradation in the ATP-dependent ubiquitin proteasome system (UPS), plays an important role in cell activity [1,2,3,4,5]
There are sufficient evidences showing that the deregulation of protein ubiquitination have been implicated in many diseases by degradation of many key regulatory proteins, including tumor suppressor, oncoprotein, and cell cycle regulator [6,7,8]
It needs emphasizing that potential ubiquitinated lysine site from other organisms can be predicted according to the results of BLAST SEARCH or Multi-species Alignment Analysis
Summary
Known as the important protein posttranslational modification of targeting proteins by ubiquitins for their subsequent degradation in the ATP-dependent ubiquitin proteasome system (UPS), plays an important role in cell activity [1,2,3,4,5]. There are sufficient evidences showing that the deregulation of protein ubiquitination have been implicated in many diseases by degradation of many key regulatory proteins, including tumor suppressor, oncoprotein, and cell cycle regulator [6,7,8]. The location, numbers, and distribution of ubiquitination site are important information for scientists to investigate the mechanism of UPS and relevant diseases [9,10]. The current available ubiquitination database like UbiProt provides information almost exclusively on yeast protein ubiquitination due to the previous experimental limits [11]. With the recent new technology advances, such as proteomic technology, mass spectrometry technology, the growing number of the experimentally confirmed ubiquitination sites of mammalian protein laid the solid basis for investigating the regulatory mechanism of protein stability. It is imperative for scientific community to construct the comprehensive database for depositing and retrieving mammalian protein ubiquitination sites
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