Summary: Ulp1 protease family, C-terminal catalytic domain
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Ulp1 protease family, C-terminal catalytic domain Provide feedback
This domain contains the catalytic triad Cys-His-Asn.
Literature references
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Mossessova E, Lima CD; , Mol Cell 2000;5:865-876.: Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. PUBMED:10882122 EPMC:10882122
Internal database links
SCOOP: | Peptidase_C5 Peptidase_C57 XFP_N |
Similarity to PfamA using HHSearch: | Peptidase_C5 |
External database links
MEROPS: | C48 |
SCOP: | 1euv |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003653
This entry represents the C-terminal part of ubiquitin-like proteases that displays full proteolytic activity [ PUBMED:10882122 ].
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 [ PUBMED:10603300 , PUBMED:8982460 ]: ubiquitin carboxyl-terminal hydrolases (UCH), ubiquitin-specific processing proteases (UBP), 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 [ PUBMED:10094048 ].
Crystal structure of yeast ULP1 bound to Smt3 [ PUBMED:10882122 ] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognise 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 alpha helices and seven beta strands. The catalytic domain includes the central alpha helix, beta-strands 4 to 6, and the catalytic triad (Cys-His-Asp).
Cysteine peptidases with a chymotrypsin-like fold are included in clan PA, which also includes serine peptidases. Cysteine peptidases that are N-terminal nucleophile hydrolases are included in clan PB. Cysteine peptidases with a tertiary structure similar to that of the serine-type aspartyl dipeptidase are included in clan PC. Cysteine peptidases with an intein-like fold are included in clan PD, which also includes asparagine lyases.
A cysteine peptidase is a proteolytic enzyme that hydrolyses a peptide bond using the thiol group of a cysteine residue as a nucleophile. Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. Cysteine peptidases can be grouped into fourteen different clans, with members of each clan possessing a tertiary fold unique to the clan. Four clans of cysteine peptidases share structural similarities with serine and threonine peptidases and asparagine lyases. From sequence similarities, cysteine peptidases can be clustered into over 80 different families [ PUBMED:11517925 ]. Clans CF, CM, CN, CO, CP and PD contain only one family.
Cysteine peptidases are often active at acidic pH and are therefore confined to acidic environments, such as the animal lysosome or plant vacuole. Cysteine peptidases can be endopeptidases, aminopeptidases, carboxypeptidases, dipeptidyl-peptidases or omega-peptidases. They are inhibited by thiol chelators such as iodoacetate, iodoacetic acid, N -ethylmaleimide or p -chloromercuribenzoate.
Clan CA includes proteins with a papain-like fold. There is a catalytic triad which occurs in the order: Cys/His/Asn (or Asp). A fourth residue, usually Gln, is important for stabilising the acyl intermediate that forms during catalysis, and this precedes the active site Cys. The fold consists of two subdomains with the active site between them. One subdomain consists of a bundle of helices, with the catalytic Cys at the end of one of them, and the other subdomain is a beta-barrel with the active site His and Asn (or Asp). There are over thirty families in the clan, and tertiary structures have been solved for members of most of these. Peptidases in clan CA are usually sensitive to the small molecule inhibitor E64, which is ineffective against peptidases from other clans of cysteine peptidases [ PUBMED:7044372 ].
Clan CD includes proteins with a caspase-like fold. Proteins in the clan have an alpha/beta/alpha sandwich structure. There is a catalytic dyad which occurs in the order His/Cys. The active site His occurs in a His-Gly motif and the active site Cys occurs in an Ala-Cys motif; both motifs are preceded by a block of hydrophobic residues [ PUBMED:9891971 ]. Specificity is predominantly directed towards residues that occupy the S1 binding pocket, so that caspases cleave aspartyl bonds, legumains cleave asparaginyl bonds, and gingipains cleave lysyl or arginyl bonds.
Clan CE includes proteins with an adenain-like fold. The fold consists of two subdomains with the active site between them. One domain is a bundle of helices, and the other a beta barrell. The subdomains are in the opposite order to those found in peptidases from clan CA, and this is reflected in the order of active site residues: His/Asn/Gln/Cys. This has prompted speculation that proteins in clans CA and CE are related, and that members of one clan are derived from a circular permutation of the structure of the other.
Clan CL includes proteins with a sortase B-like fold. Peptidases in the clan hydrolyse and transfer bacterial cell wall peptides. The fold shows a closed beta barrel decorated with helices with the active site at one end of the barrel [ PUBMED:14725770 ]. The active site consists of a His/Cys catalytic dyad.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | cysteine-type peptidase activity (GO:0008234) |
Biological process | proteolysis (GO:0006508) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Peptidase_CA (CL0125), which has the following description:
This clan includes peptidases with the papain-like fold.
The clan contains the following 78 members:
Acetyltransf_2 Amidase_5 Amidase_6 BtrH_N CHAP CIF CoV_peptidase DUF1175 DUF1287 DUF1460 DUF2026 DUF2145 DUF2272 DUF3335 DUF553 EDR1 Gln_amidase Gln_deamidase_2 Guanylate_cyc_2 Herpes_teg_N Josephin LRAT Mac-1 Menin NLPC_P60 Nt_Gln_amidase OTU Peptidase_C1 Peptidase_C10 Peptidase_C101 Peptidase_C12 Peptidase_C16 Peptidase_C1_2 Peptidase_C2 Peptidase_C21 Peptidase_C23 Peptidase_C27 Peptidase_C28 Peptidase_C31 Peptidase_C32 Peptidase_C33 Peptidase_C34 Peptidase_C36 Peptidase_C39 Peptidase_C39_2 Peptidase_C42 Peptidase_C47 Peptidase_C48 Peptidase_C5 Peptidase_C54 Peptidase_C58 Peptidase_C6 Peptidase_C65 Peptidase_C7 Peptidase_C70 Peptidase_C71 Peptidase_C78 Peptidase_C8 Peptidase_C9 Peptidase_C92 Peptidase_C93 Peptidase_C97 Peptidase_C98 Phytochelatin Rad4 SidE_DUB Tae4 TGase_elicitor TGL Tox-PL-2 Tox-PLDMTX Transglut_core Transglut_core2 Transglut_core3 Transglut_prok UCH UCH_1 VasohibinAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (27) |
Full (20417) |
Representative proteomes | UniProt (33495) |
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RP15 (3130) |
RP35 (9037) |
RP55 (15278) |
RP75 (21732) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (27) |
Full (20417) |
Representative proteomes | UniProt (33495) |
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RP15 (3130) |
RP35 (9037) |
RP55 (15278) |
RP75 (21732) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Structural domain |
Previous IDs: | Ulp1_C; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Griffiths-Jones SR |
Number in seed: | 27 |
Number in full: | 20417 |
Average length of the domain: | 164.1 aa |
Average identity of full alignment: | 15 % |
Average coverage of the sequence by the domain: | 29.81 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 216 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Peptidase_C48 domain has been found. There are 80 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.