PROSITE documentation PDOC52064Ubiquitin-binding motif (UBM) domain profile
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PURL: https://purl.expasy.org/prosite/documentation/PDOC52064
Ubiquitin (Ub) plays a major role in regulating diverse biological pathways by changing the function, localization, or turnover of target proteins. Signaling through Ub is generally thought to occur by low-affinity noncovalent interactions between Ub and a variety of specialized Ub-binding domains (UBDs). UBDs can be classified into a number of different families, whose members share sequence and structural similarity only within the families, but not between them. The ubiquitin-binding motif (UBM) domain is an UBD that is present in Y-family polymerases iota (POLI) and REV1, both of which contain two UBMs at the C-terminus, the DNA repair protein XPG/ERCC5 (corresponding to budding yeast Rad2 and fission yeast Rad13) which contains a UBM domain and the RING-type ubiquitin ligase MULE/HUWE1 (corresponding to budding yeast Tom1) which contains three UBM copies. UBM domains bind any accessible ubiquitin interface in monoubiquitin or ubiquitin chains [1,2,3,4,5,6].
The UBM domain spans ~35 residues and consists of a helix-turn-helix motif where the first helix is longer than the second, and the turn is comprised of a highly conserved Leu-Pro motif that is poised for interaction with ubiquitin (see <PDB:2KHU>) [3,4,5,6].
The profile we developed covers the entire UBM domain.
Last update:June 2025 / First entry.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Bienko M. Green C.M. Crosetto N. Rudolf F. Zapart G. Coull B. Kannouche P. Wider G. Peter M. Lehmann A.R. Hofmann K. Dikic I. |
| Title | Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. | |
| Source | Science 310:1821-1824(2005). | |
| PubMed ID | 16357261 | |
| DOI | 10.1126/science.1120615 |
| 2 | Authors | Hofmann K. |
| Title | Ubiquitin-binding domains and their role in the DNA damage response. | |
| Source | DNA Repair. (Amst). 8:544-556(2009). | |
| PubMed ID | 19213613 | |
| DOI | 10.1016/j.dnarep.2009.01.003 |
| 3 | Authors | Bomar M.G. D'Souza S. Bienko M. Dikic I. Walker G.C. Zhou P. |
| Title | Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases iota and Rev1. | |
| Source | Mol. Cell. 37:408-417(2010). | |
| PubMed ID | 20159559 | |
| DOI | 10.1016/j.molcel.2009.12.038 |
| 4 | Authors | Cui G. Benirschke R.C. Tuan H.-F. Juranic N. Macura S. Botuyan M.V. Mer G. |
| Title | Structural basis of ubiquitin recognition by translesion synthesis DNA polymerase iota. | |
| Source | Biochemistry 49:10198-10207(2010). | |
| PubMed ID | 21049971 | |
| DOI | 10.1021/bi101303t |
| 5 | Authors | Suzuki N. Hiraki M. Yamada Y. Matsugaki N. Igarashi N. Kato R. Dikic I. Drew D. Iwata S. Wakatsuki S. Kawasaki M. |
| Title | Crystallization of small proteins assisted by green fluorescent protein. | |
| Source | Acta Crystallogr. D. Biol. Crystallogr. 66:1059-1066(2010). | |
| PubMed ID | 20944239 | |
| DOI | 10.1107/S0907444910032944 |
| 6 | Authors | Burschowsky D. Rudolf F. Rabut G. Herrmann T. Peter M. Wider G. |
| Title | Structural analysis of the conserved ubiquitin-binding motifs (UBMs) of the translesion polymerase iota in complex with ubiquitin. | |
| Source | J. Biol. Chem. 286:1364-1373(2011). | |
| PubMed ID | 20929865 | |
| DOI | 10.1074/jbc.M110.135038 |
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