{PDOC52064}
{PS52064; UBM}
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* Ubiquitin-binding motif (UBM) domain profile *
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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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: June 2025 / First entry.

[ 1] 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.
     "Ubiquitin-binding domains in Y-family polymerases regulate
     translesion synthesis."
     Science 310:1821-1824(2005).
     PubMed=16357261; DOI=10.1126/science.1120615
[ 2] Hofmann K.
     "Ubiquitin-binding domains and their role in the DNA damage
     response."
     DNA Repair. (Amst). 8:544-556(2009).
     PubMed=19213613; DOI=10.1016/j.dnarep.2009.01.003
[ 3] Bomar M.G., D'Souza S., Bienko M., Dikic I., Walker G.C., Zhou P.
     "Unconventional ubiquitin recognition by the ubiquitin-binding motif
     within the Y  family DNA polymerases iota and Rev1."
     Mol. Cell. 37:408-417(2010).
     PubMed=20159559; DOI=10.1016/j.molcel.2009.12.038
[ 4] Cui G., Benirschke R.C., Tuan H.-F., Juranic N., Macura S.,
     Botuyan M.V., Mer G.
     "Structural basis of ubiquitin recognition by translesion synthesis
     DNA polymerase  iota."
     Biochemistry 49:10198-10207(2010).
     PubMed=21049971; DOI=10.1021/bi101303t
[ 5] Suzuki N., Hiraki M., Yamada Y., Matsugaki N., Igarashi N., Kato R.,
     Dikic I., Drew D., Iwata S., Wakatsuki S., Kawasaki M.
     "Crystallization of small proteins assisted by green fluorescent
     protein."
     Acta Crystallogr. D. Biol. Crystallogr. 66:1059-1066(2010).
     PubMed=20944239; DOI=10.1107/S0907444910032944
[ 6] Burschowsky D., Rudolf F., Rabut G., Herrmann T., Peter M., Wider G.
     "Structural analysis of the conserved ubiquitin-binding motifs (UBMs)
     of the  translesion polymerase iota in complex with ubiquitin."
     J. Biol. Chem. 286:1364-1373(2011).
     PubMed=20929865; DOI=10.1074/jbc.M110.135038

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