In eukaryotes, ubiquitin and other ubiquitin-like (Ub/UBL) modifications share a similar three-step thioester cascade process catalyzed by E1s (ubiquitin-activating enzymes), E2s (ubiquitin-conjugating enzymes) and E3s (ubiquitin-protein ligases) (Kerscher et al., 2006). The process of Ub/UBL conjugation is reversed by DUBs (deubiquitinating enzymes), which could remove the Ub/UBL from modified proteins (Nijman et al., 2005; Reyes-Turcu et al., 2009). Moreover, UBDs (ubiquitin-binding domain containing proteins) can selectively recognize monoubiquitin and ubiquitin chains with different linkages and lengths to control various cellular functions in vivo (Husnjak et al., 2012). Besides, ULDs (ubiquitin like domains) are also identified as important integral elements of a large variety of protein families (Upadhya SC et al., 2003). Owe to the complexity of ubiquitin signal formation and its corresponding recognition mechanism, ubiquitination performs various cellular and physiological functions.
The released UUCD 2.0 (Ubiquitin and Ubiquitin-like Conjugation Database, ver 2.0) is an updated systematic resource for ubiquitin and ubiquitin-like conjugation. 26 E1s, 109 E2s, 1,153 E3s, 151 DUBs, 392 UBDs and 184 ULDs were collected from scientific literatures and classified into 1, 4, 22, 7, 25, 11 families, respectively. The 2.0 release added 4 new families for E2 and E3 enzymes, including Autophagy_C, PHD, A20 and DCUN1 (Yamaguchi et al., 2012; Wang et al., 2012; Ali et al., 2014; Kang et al., 2013; Mergner et al., 2014; Shin et al., 2012). Specially, we constructed a hierarchical classification for UBD and ULD families. From 148 eukaryotic species, 129,416 proteins were identified as unique entries in UUCD 2.0.
For publication of results please cite the following article:
UUCD: a family-based 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.
UUCD 2.0: an updated database of regulators for ubiquitin and ubiquitin-like conjugation
Jiaqi Zhou, Wankun Deng, Shaofeng Lin, Chenwei Wang, Yang Xu, Haodong Xu, Shuang Zhang, Ying Zhang, and Yu Xue.