To improve security and privacy, we are moving our web pages and services from HTTP to HTTPS.
To give users of web services time to transition to HTTPS, we will support separate HTTP and HTTPS services until the end of 2017.
From January 2018 most HTTP traffic will be automatically redirected to HTTPS. [more...]
View this page in https
PROSITE documentation PDOC50600 [for PROSITE entry PS50600]

Ubiquitin-like protease family profile


Deubiquitinating enzymes (DUB) form a large family of cysteine protease that can deconjugate ubiquitin or ubiquitin-like proteins from ubiquitin-conjugated proteins. They can be classified in 3 families according to sequence homology [1,2]: ubiquitin carboxyl-terminal hydrolases (UCH) (see <PDOC00127>), ubiquitin-specific processing proteases (UBP) (see <PDOC00750>), and ubiquitin-like proteases (ULP) (EC specific for deconjugating ubiquitin-like proteins. In contrast to the UBP pathway, which is very redundant (16 UBP enzymes in yeast), there is few ubiquitin-like protease (only one in yeast, ULP1).

ULP1 catalyses two critical functions in the SUMO/Smt3 pathway via its cysteine protease activity. ULP1 processes the Smt3 C-terminal sequence (-GGATY) to its mature form (-GG), and it deconjugates Smt3 from the lysine epsilon-amino group of the target protein [3].

Crystal structure of yeast ULP1 bound to Smt3 [4] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognize the Gly-Gly motif at the C-terminal extremity of Smt3 protein. Ulp1 adopts a novel architecture despite some structural similarity with other cysteine protease. The secondary structure is composed of seven α helices and seven β strands. The catalytic domain includes the central α helix, β-strands 4 to 6, and the catalytic triad (Cys-His-Asp) (see <PDB:1EUV>).

We developed a profile directed against the C-terminal part of ULP proteins that displays full proteolytic activity [4].


These proteins belong to family C48 in the classification of peptidases [E1].

Last update:

May 2008 / Text revised.

Technical section

PROSITE method (with tools and information) covered by this documentation:

ULP_PROTEASE, PS50600; Ubiquitin-like protease family profile  (MATRIX)


1AuthorsChung C.H., Baek S.H.
TitleDeubiquitinating enzymes: their diversity and emerging roles.
SourceBiochem. Biophys. Res. Commun. 266:633-640(1999).
PubMed ID10603300

2AuthorsHochstrasser M.
TitleUbiquitin-dependent protein degradation.
SourceAnnu. Rev. Genet. 30:405-439(1996).
PubMed ID8982460

3AuthorsLi S.J., Hochstrasser M.
TitleA new protease required for cell-cycle progression in yeast.
SourceNature 398:246-251(1999).
PubMed ID10094048

4AuthorsMossessova E., Lima C.D.
TitleUlp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast.
SourceMol. Cell 5:865-876(2000).
PubMed ID10882122


PROSITE is copyright. It is produced by the SIB Swiss Institute Bioinformatics. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement. For information about the licensing scheme send an email to
Prosite License or see: prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)