Table 1. Ubiquitin binding domains (See text and [48-53] for details).
| Structure | Domain | Comments |
|---|---|---|
| Single Helices | UIM | Binds to groove on ubiquitin containing hydrophobic patch |
| DUIM | Double UIM | |
| MIU | Binds to groove on ubiquitin but in opposite orientation | |
| Three helix bundles | UBA | Widespread, often combined with other ubiquitin-binding domains |
| CUE | UBA variant involved in ERAD | |
| VHS | Seven helices in folded domain, endosomal sorting | |
| GAT | Found in endosomal sorting pathways, UBA+2 ZnF | |
| Zinc Fingers | NZF | Found in Npl4, TAB2, and NZF2 of ESCRT II |
| ZnF UBP | Found in deubiquitinating enzymes, BRAP2 ligase and HDAC6 | |
| A20 ZnF | Variant of ZnF ubiquitin-specific protease domain, found in A20 deubiquitinating enzyme and Rabex 5 | |
| UBZ | Found in Y-family polymerases involved in DNA repair | |
| Catalytic Domains | UBC | Catalytic domain of E2 ubiquitin-conjugating enzymes |
| UEV | Variant UBC lacking enzymatic Cys residue, inactive | |
| SENP | SUMO-specific protease domain | |
| USP | Ubiquitin-specific protease deubiquitinating enzyme domain | |
| UCH | Ubiquitin C-terminal hydrolase deubiquitinating enzyme domain | |
| OTU | Ovarian Tumor-related deubiquitinating enzyme domain | |
| Jab1/MPN | Metalloprotease deubiquitinating enzymes | |
| Other Domains | GLUE | GRAM-like ubiquitin-binding domain in EAP45 |
| PRU | PH domain of RPN13 | |
| SH3 | SH3 domain in many endocytic proteins | |
| UBM | Ubiquitin-binding domain in Y-family DNA polymerases | |
| PFU | Ubiquitin-binding domain of PLAA family proteins | |
| WD40 | WD40 domain of UFD2/DOA1/PLAA | |
| UBAN | Coiled Coil, binds to Met1-linked polyubiquitin |
Abbreviations: DOA1, degradation of alpha2 1; ERAD, endoplasmic reticulum-associated protein degradation; GLUE, GRAM-like ubiquitin-binding domain in EAP45; MIU, ubiquitin interacting domain; NZF, Npl4 zinc fingers; OTU, Ovarian Tumor; PFU, PLAA family ubiquitin binding domain; PH, pleckstin homology; PLAA, phospholipase A2 activating protein; SUMO, small ubiquitin-like modifier; UBA, ubiquitin associated; UBAN, ubiquitin binding in ABIN and NEMO proteins; UBC, ubiquitin C; UBM, ubiquitin-binding motif; UBP, ubiquitin-specific protease domain; UIM, ubiquitin interacting motif; UBZ, ubiquitin-binding zinc finger; UCH, ubiquitin C-terminal hydrolase; UEV, ubiquitin E2 variant; UFD2, ubiquitin fusion degradation 2; USP, ubiquitin-specific protease; ZnF zinc fingers.