The 2004 Nobel Prize in Chemistry was awarded for the discovery of ubiquitin and ubiquitin proteasome system that is a highly-specific, ATP-dependent pathway responsible for targeting specific proteins for degradation. Ubiquitin is a small protein comprising 76 amino acids in eucaryote from plants and fungi to mammals. It makes a large variety of functions because it can be conjugated to target proteins and lead to their destruction (Hershko 1983; Hershko et al., 1975).

     Ubiquitination is one of the most important post-translational modifications. There are usually three enzymes, E1, E2 and E3 (Scheffner et al., 1995), which mediate the process. E1, named "ubiquitin-activating enzyme" (Haas et al., 1982), first activates ubiquitin, transfers it to its active site Cys. ATP is required as an energy source for the transfer (Ciechanover et al., 1980; Hershko et al., 1979). Secondly, E2, named "ubiquitin-conjugating enzyme", binds E1 and conjugates the ubiquitin molecule from E1 to the site active Cys of E2 itself. The ubiquitin is then passed on to the target protein, via a final critical E3, named "ubiquitin ligase", which recognizes the substrate and provides it with the ubiquitin (Deshaies et al., 2009). The substrate is attached with a polyubiquitin chain via repeats of the whole process and is finally taken to the proteasome for degradation (Hershko et al., 1992). As the ubiquitination cascade process runs, specificity increases: E1 binds tens of E2s, which have a number of well-conserved domains and interact with more limited hundreds of E3s, which share less conserved motifs that can specifically recognize and bind more target proteins. Other ubiquitin-like modifications, including SUMOylation, Neddylation, ISGylation, Pupylation, share the same E1-E2-E3 cascade (Hochstrasser et al., 2009). The process can be reversed that requires DUBs (deubiquitinating enzymes) to cleave ubiquitin or ubiquitin-like from the substrate (Nijman et al., 2005; Reyes-Turcu et al., 2009).

    The ubiquitin system also has many non-proteolytic functions (Chen et al., 2009), which depent on the additon of single ubiquitin (monoubiquitination) (Polo et al., 2002), types of polyubiquitin chain (polyubiquitination), and particular self-ubiquitination (de Bie et al., 2011). Monoubiquitination and Lys63-linked polyubiquitylation have several nonproteolytic functions in many cell signalling pathways, such as membrane trafficking (Hurley et al., 2011), protein activation and transactivation (Wang et al., 2001; Polo et al., 2002), DNA replication and repair (Ulrich et al., 2010), and chromatin dynamics (Smolle et al., 2011). Compared to ubiquitination, many ubiquitin-like modifications usually make non-degradative functions (Mishra et al., 2011; Hochstrasser et al., 2000; Welchman et al., 2005).

    Although the investigation of ubiquitin and ubiquitin-like conjugation has advanced with thousands of works, a veracious and detailed experimentally confirmed numbers of the E1s, E2s, E3s and DUBs, the comprehensive classification of these enzymes and how many potential E1s, E2s, E3s and DUBs exist in usual and rare species still remains not to be available. In this work, we have collected all experimental enzymes of the ubiquitin and ubiquitin-like conjugation systems from all the related literature of PubMed and predicted all the potential E3s or subunits of complex E3s in 70 species, which cover the plants, fungi and animals. Especially there are 1,017 E3 ligases collected with 486 existing in human. Based on characteristics of domains, we classified all known E1s, E2s, E3s and DUBs into a hierarchical structure with four levels, such as class, subclass, family and single protein. Then we built ten main classes consisting of E1 (Schulman et al., 2009; Jones et al., 2002), E2 (Jones et al., 2002), HECT (Rotin et al., 2009), RING (Deshaies et al., 2009), N-recognin (Tasaki 2009; Choi et al., 2010), Cullin RING (Hotton et al., 2008; Petroski et al., 2005), APC/C (Schreiber et al., 2011), DUB (Reyes-Turcu et al., 2009) and two classes named "Other", which belong to single protein ligases and subunits of complex ligases, respectively. Moreover, all enzymes can be further divided into 34 families. 28 of 34 families enable us to build corresponding HMM proflies, which are used to predict new potential enzymes. The Ubiquitin and Ubiquitin-like Conjugation Database (UUCD) is the most integrative and comprehensive resource for users to systematically search for each enzyme and generate a integrative view of enzyme cascades in ubiquitin and ubiquitin-like conjugation systems.

    The UUCD 1.0 database was updated on Jun. 27th, 2012, containing 57,015 unique protein entries. The online service of UUCD 1.0 was implemented in PHP + MySQL + JavaScript + Perl. The database will be updated routinely as new UUCD proteins are reported.

For publication of results please cite the following article:

UUCD: a comprehensive database of ubiquitin and ubiquitin-like conjugation
  Tianshun Gao, Zexian Liu, Yongbo Wang, Han Cheng, Qing Yang, Anyuan Guo,  
Jian Ren
  and Yu Xue. Nucleic Acids Research. 2013, 41:D445-D451.

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