※ INTRODUCTION:

    In eukaryotes, ubiquitin and other ubiquitin-like (Ub/UBL) modifications share a similar E1 (ubiquitin-activating enzyme)- E2 (ubiquitin-conjugating enzyme)- E3 (ubiquitin-protein ligase) enzyme cascade (Kerscher et al., 2006). The process of Ub/UBL conjugation is reversed by DUB (deubiquitinating enzyme), which could move the Ub/UBL from modified proteins (Nijman et al., 2005; Reyes-Turcu et al., 2009). Generally, ubiquitin signaling has a specificity that is conferred by alternative conjugation types (monoubiquitin and polyubiquitin) and interactions with UBD (ubiquitin-binding domain) containing proteins, which selectively recognize monoubiquitin and ubiquitin chains with different linkages and length 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. A large number of proteins combine a ULD with a UBD within the same region and promote the degradation of ubiquitinated proteins through interaction with substrate by UBD and binding proteasome by ULD (Grabbe et al., 2009).

    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, 1,211 E3s, 153 DUBs, 424 UBDs and 186 ULDs were collected from experiments 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 (E2 of ATG8 and ATG12), PHD, A20 and DCUN1 (E3 of NEDD8) (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 protein were identified as unique entries in UUCD 2.0.




    

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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.

[Abstract] [Full Text(HTML)] [Full Text(PDF)][Supplemental Data]


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.

[Abstract] [Full Text(HTML)] [Full Text(PDF)][Supplemental Data]