| UBD . | Ubiquitin binding mode . | Number of UBD-containing proteins (cell cycle associated/total) . | Examples with cell cycle functions . | Ubiquitin-binding role in cell cycle functiona . | Reference . |
|---|---|---|---|---|---|
| UBA | MonoUb, polyUb (predominant for K48) | 14/55 | UBQLN2,b KPC2,b,c FAF1,d UBASH3B,c BRSK1/2, LATS1/2, MARK4 | KPC2 (E3 ligase subunit): Promotes the transfer of ubiquitylated p27 to the proteasome; UBASH3B: Targets ubiquitylated Aurora B to microtubules in mitosis | Hara et al., 2005; Krupina et al., 2016 |
| CUE | MonoUb | 1/13 | CUEDC2c | CUEDC2: Promotes MCC release from APC/CCDC20 | Gao et al., 2011 |
| UIM | MonoUb, polyUb (K48, K63) | 6/28 | DDI1,b RPN10,b Epsin-1, MAT1, alpha4c | alpha4: Prevents polyubiquitylation of the PP2A catalytic subunit | Kong et al., 2009; McConnell et al., 2010 |
| UBP | PolyUb | 1/3 | USP39 | None described | — |
| NZF | MonoUb, polyUb (K63) | 2/7 | NPL4,d HOIL-1 | None described | — |
| UEV | MonoUb | 1/2 | TSG101 | None described | — |
| UBAN | DimonoUb (M1) | 2/7 | ALIX, Optineurin | None described | — |
| WD40 (subset) | MonoUb | 1/4 | BUB3 | None described | — |
| Unique or uncharacterized domains | Various | 10/21 | RPN13,b VCP,d UFD1,d NUP62, ERα, SMURF2c | SMURF2 (E3 ligase): Stabilize ubiquitylated substrate binding to promote polyUbe | Ogunjimi et al., 2010 |
| Domains not found in cell cycle regulators | Various | 0/22 | — | — | — |
| Total | — | 38/162 | — | — | — |
| UBD . | Ubiquitin binding mode . | Number of UBD-containing proteins (cell cycle associated/total) . | Examples with cell cycle functions . | Ubiquitin-binding role in cell cycle functiona . | Reference . |
|---|---|---|---|---|---|
| UBA | MonoUb, polyUb (predominant for K48) | 14/55 | UBQLN2,b KPC2,b,c FAF1,d UBASH3B,c BRSK1/2, LATS1/2, MARK4 | KPC2 (E3 ligase subunit): Promotes the transfer of ubiquitylated p27 to the proteasome; UBASH3B: Targets ubiquitylated Aurora B to microtubules in mitosis | Hara et al., 2005; Krupina et al., 2016 |
| CUE | MonoUb | 1/13 | CUEDC2c | CUEDC2: Promotes MCC release from APC/CCDC20 | Gao et al., 2011 |
| UIM | MonoUb, polyUb (K48, K63) | 6/28 | DDI1,b RPN10,b Epsin-1, MAT1, alpha4c | alpha4: Prevents polyubiquitylation of the PP2A catalytic subunit | Kong et al., 2009; McConnell et al., 2010 |
| UBP | PolyUb | 1/3 | USP39 | None described | — |
| NZF | MonoUb, polyUb (K63) | 2/7 | NPL4,d HOIL-1 | None described | — |
| UEV | MonoUb | 1/2 | TSG101 | None described | — |
| UBAN | DimonoUb (M1) | 2/7 | ALIX, Optineurin | None described | — |
| WD40 (subset) | MonoUb | 1/4 | BUB3 | None described | — |
| Unique or uncharacterized domains | Various | 10/21 | RPN13,b VCP,d UFD1,d NUP62, ERα, SMURF2c | SMURF2 (E3 ligase): Stabilize ubiquitylated substrate binding to promote polyUbe | Ogunjimi et al., 2010 |
| Domains not found in cell cycle regulators | Various | 0/22 | — | — | — |
| Total | — | 38/162 | — | — | — |
We considered UBD-containing proteins annotated in UniProtKB/Swiss-Prot, a curated protein database (UniProt Consortium, 2015), together with a manual literature search. Our criteria include (1) proteins containing UBDs described previously (Husnjak and Dikic, 2012), (2) other proteins annotated as binding ubiquitin, and (3) manual exclusion in case of covalent ubiquitin binding (e.g., E2s or ubiquitin modification) and of active DUBs. Assignment of cell cycle–related functions was determined by gene ontology and complemented with manual literature search. Ubiquitin-binding mode is according to Husnjak and Dikic (2012). MonoUb, monoubiquitylation; polyUb, polyubiquitylation; —, not applicable.
Excluding proteins involved in general proteasome function or that of VCP/p97.
Proteasome subunit, or proteasome associated (mostly according to Grice and Nathan, 2016).
Proteins have a reported cell cycle function for their UBDs that is distinct from general proteasome or VCP/p97 functions.
VCP/p97 component or cofactor (Meyer et al., 2012).
Probably a general mechanism, which includes its cell cycle functions.