Family C48


Summary Holotypes Alignment Tree Genomes Structure Literature H-seq M-seq

Summary for family C48

NamePeptidase family C48 (Ulp1endopeptidase family)
Family type peptidaseC48.001 - Ulp1 peptidase (Saccharomyces cerevisiae), MEROPS Accession MER0005202 (peptidase unit: 439-592)
Content of familyPeptidase family C48 contains SUMO (small ubiquitin-like modifier) deconjugating enzymes.
History Identifier created: MEROPS 5.00 (20 April 2000)
SUMO proteins are a group of proteins that are related to ubiquitin both in their structure and way in which they are ligated. However, unlike ubiquitinated proteins, sumolated proteins do not tend to be degraded. Instead SUMO and Smt3 (the yeast equivalent) have been implicated in the targeting of protein for export from the nucleus. The members of peptidase family C48 are involved in the processing of SUMO precursors and in the deconjugation of SUMO proteins from cellular targets. Families C97 and C98 also contain peptidases that release SUMO from conjugated proteins (Hickey et al., 2012).
Catalytic typeCysteine
Active site residuesH514 D531 Q574 C580 
Active siteThe catalytic Cys580 is coordinated by His514, which is stabilized by Asp531. Cys580 and Gln574 form the oxyanion hole (Mossenova & Lima, 2000).
Activities and specificitiesUlp1 peptidase (C48.001) demonstrates dual enzymic activity different to most deubiquitinating enzymes. Firstly, Ulp1 processes the Smt3 precursor into its mature form, cleaving after a Gly-Gly motif. Secondly, Ulp1 cleaves the peptide bond formed between the C-terminal Gly of the mature Smt3 and the lysine epsilon-amino groups of target proteins. It has been demonstrated that Ulp1 can recognise the substrate of SENP1 (C48.002), SUMO-1 (Li & Hochstrasser, 1999).
InhibitorsUlp1 peptidase is sensitive to inhibition by ubiquitin aldehyde (Lima, 2004).
Molecular structureUlp1 peptidase shows similarity to the tertiary structure of adenain (C05.001). Trp448 and Trp515 enable the formation of a constricted VDW tunnel to interact with the C-terminal Smt3 Gly-Gly motif (Mossenova & Lima, 2000). Surprisingly, the three families of deSUMOlatying peptidases are members of three different clans despite being the same catalytic type.
Basis of clan assignmentProtein fold of the peptidase unit for members of this family resembles that of adenain, the type example for clan CE.
Distribution of family Bacteria details  
Archaea details  
Protozoa details  
Fungi details  
Plants details  
Animals details  
Viruses details  
Biological functionsSuggested roles for SUMO type proteins include the regulation of nucleocytoplasmic transport or in processes coordinating SUMO modification on entry or exit from the nucleus via the nuclear pore complex protein RANB2 (Lima, 2004).
Statistics for family C48Sequences:5954
Identifiers with PDB entries:5
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
Ulp1 peptidaseC48.001Yes
SENP1 peptidaseC48.002Yes
SENP3 peptidaseC48.003-
SENP6 peptidaseC48.004-
Ulp2 peptidaseC48.005-
SENP2 peptidaseC48.007Yes
SENP5 peptidaseC48.008-
SENP7 peptidaseC48.009Yes
SUSP4 peptidase (Mus musculus)C48.010-
SENP8 peptidaseC48.011-
SENP4 peptidaseC48.012-
Mername-AA145 peptidaseC48.013-
Mername-AA147 peptidaseC48.014-
Mername-AA148 peptidaseC48.015-
Mername-AA149 peptidaseC48.016-
Mername-AA150 peptidaseC48.017-
peptidase similar to SUMO-1-specific peptidase (Rattus norvegicus)C48.018-
LOC297623 peptidase (Rattus norvegicus)C48.020-
similar to SUMO-1-specific peptidase (Mus musculus)C48.021-
ESD4 peptidaseC48.022-
XopD peptidaseC48.023-
Ulp1 peptidase (Drosophila-type)C48.024-
Nep1 peptidase (Schizosaccharomyces sp.)C48.025-
573K1.5 peptidaseC48.026-
Mername-AA233 putative peptidase (Mus musculus)C48.027-
sentrin-specific peptidase 14 (Mus musculus)C48.028-
sentrin-specific peptidase 15 (Mus musculus)C48.029-
sentrin-specific peptidase 17 (Rattus norvegicus)C48.030-
SENP8 peptidase (fungus-type)C48.031-
ChlaDub1 peptidaseC48.032-
ChlaDub2 peptidaseC48.033-
PfSENP1 (Plasmodium falciparum)C48.034-
Mername-AA146 proteinC48.971-
At4g00690 (Arabidopsis thaliana)C48.A01-
At3g06910 (Arabidopsis thaliana)C48.A02-
At5g60190 (Arabidopsis thaliana)C48.A03-
At1g60220 (Arabidopsis thaliana)C48.A04-
At1g10570 (Arabidopsis thaliana)C48.A05-
CG12717 protein (Drosophila melanogaster)C48.A06-
CG10107 protein (Drosophila melanogaster)C48.A07-
CG11023 protein (Drosophila melanogaster)C48.A08-
ulp2 protein (Schizosaccharomyces pombe-type)C48.A09-
ulp-7 g.p. (Caenorhabditis elegans)C48.A10-
T27C5.9 transposon (Caenorhabditis elegans)C48.A11-
ulp-2 g.p. (Caenorhabditis elegans)C48.A12-
ulp-3 g.p. (Caenorhabditis elegans)C48.A13-
Y48A5A.1 g.p. (Caenorhabditis elegans)C48.A14-
ulp-1 g.p. (Caenorhabditis elegans)C48.A15-
ulp-4 g.p. (Caenorhabditis elegans)C48.A16-
DDB_G0293508 (Dictyostelium discoideum)C48.A17-
DDB_G0292290 (Dictyostelium discoideum)C48.A18-
ulp1 peptidase (Schizosaccharomyces pombe-type)C48.A19-
MAL8P1.157 g.p. (Plasmodium falciparum)C48.A20-
LOC559077 g.p. (Brachydanio rerio)C48.A21-
LOC571373 g.p. (Brachydanio rerio)C48.A22-
pseudogene (Mus musculus chromosome 2)C48.P01-
LOC625377 pseudogene (Mus musculus chromosome 14)C48.P02-
family C48 non-peptidase homologuesnon-peptidase homologue-
family C48 unassigned peptidasesunassignedYes