mUbiSiDa - Database of mammalian protein ubiquitination site
About ubiquitinations

Introduction
1. What is ubiquitination
Ubiquitin is a small regulatory protein firstly identified in 1975, with a molecular mass of about 8.5 kDa, and the length of 76 amino acid residues highly conserved in all eukaryotic cells. Ubiquitin can be attached to specific lysine residues of target proteins by forming isopeptide bonds and label them for destruction in 26S proteosome with the aid of activating enzyme (E1), conjugating enzyme (E2), and ubiquitin ligase (E3). Ubiquitination is an enzymatic, protein post-translational modification (PTM) process, which plays important regulatory roles in many cell functions, such as DNA repair and transcription, protein degradation, endocytosis and cell division. The attachment to target protein by one or more ubiquitins plays a pivotal regulatory mechanism in cell activities. Therefore the location, numbers, and distribution of ubiquitination site is essential for comprehensively understanding the regulation of the complex Ubiquitination system and the molecular mechanisms of cell functions.
2. Protein Ubiquitination Pathway
Protein ubiquitination in eukaryotic cell regulates most intracellular life activities by degradating many key regulatory proteins including tumor suppressor, oncoprotein, and cell cycle. Ubiquitin-Proteasome Pathway is a complex and multistep process, involving a highly organized cascade of enzymatic reactions that select, mark, and degrades proteins. Firstly the ubiquitination pathway is activated by attaching C-terminal residue of ubiquitin to a Cys sulphydryl residue in E1 enzyme. Then ubiquitin attached to an E1 is transferred to an E2, which can be conjugated with various E3s. Ub-protein ligase E3 recognizes a specific protein substrate and catalyzes the transfer of activated Ub to it. In the end, the substrate is sent to 26S proteasome for degradation. (Figure1 Protein Ubiquitination Pathway)
Figure1. Protein Ubiquitination Pathway
 


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