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2  structures 1396  species 0  interactions 4831  sequences 108  architectures

Family: Peptidase_C97 (PF05903)

Summary: PPPDE putative peptidase domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

PPPDE putative peptidase domain Provide feedback

The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p) [1].

Literature references

  1. Iyer LM, Koonin EV, Aravind L; , Cell Cycle 2004;3:1440-1450.: Novel predicted peptidases with a potential role in the ubiquitin signaling pathway. PUBMED:15483401 EPMC:15483401


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008580

The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of thiol peptidases with a circularly permuted papain-like fold. They contain a PPPDE domain which is a cysteine isopeptidase that exhibits a deSUMOylase activity in PPPDE2 (DeSI-1) and a deubiquinating activity in PPPDE1 (DeSI-2) and is described as a mixed alpha/beta-fold composed of six beta-strands and six alpha-helices. The catalytic dyad is formed by a conserved N-terminal histidine residue on beta2-strand and a conserved C-terminal cysteine residue on the following alpha3-helix (the H-C configuration). This catalytic dyad is invariably conserved in the PPPDE family of proteins [ PUBMED:15483401 , PUBMED:22498933 , PUBMED:28483520 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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...

View options

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
(30)
Full
(4831)
Representative proteomes UniProt
(12641)
RP15
(874)
RP35
(2428)
RP55
(3931)
RP75
(5229)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(30)
Full
(4831)
Representative proteomes UniProt
(12641)
RP15
(874)
RP35
(2428)
RP55
(3931)
RP75
(5229)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(30)
Full
(4831)
Representative proteomes UniProt
(12641)
RP15
(874)
RP35
(2428)
RP55
(3931)
RP75
(5229)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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.

Note: You can also download the data file for the tree.

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 View help on the curation process

Seed source: L. Iyer
Previous IDs: DUF862;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 30
Number in full: 4831
Average length of the domain: 135.10 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 43.19 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.2 29.2
Trusted cut-off 29.2 29.4
Noise cut-off 29.1 29.1
Model length: 151
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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_C97 domain has been found. There are 2 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.

Protein Predicted structure External Information
A0A0P0VQG1 View 3D Structure Click here
A0A0P0WS35 View 3D Structure Click here
A0A0P0WTV3 View 3D Structure Click here
A0A0R0JKA3 View 3D Structure Click here
A0A1D6GPN1 View 3D Structure Click here
A0A1D6HP63 View 3D Structure Click here
A0A1D6JJK7 View 3D Structure Click here
A0A1D6NTT5 View 3D Structure Click here
A0A2R8QHD8 View 3D Structure Click here
A0A2R8QHR3 View 3D Structure Click here
A4HU52 View 3D Structure Click here
A4HU53 View 3D Structure Click here
A4I0Q3 View 3D Structure Click here
A4I7V0 View 3D Structure Click here
B4FIH1 View 3D Structure Click here
B4FMU4 View 3D Structure Click here
B4FNK3 View 3D Structure Click here
B4FXF6 View 3D Structure Click here
B6T7H3 View 3D Structure Click here
B6TH05 View 3D Structure Click here
C0HDP7 View 3D Structure Click here
C6T0E5 View 3D Structure Click here
C6TA34 View 3D Structure Click here
C6TAJ5 View 3D Structure Click here
C6TDS4 View 3D Structure Click here
C6TEF8 View 3D Structure Click here
C6THR3 View 3D Structure Click here
C6TMS7 View 3D Structure Click here
E9AHP5 View 3D Structure Click here
H2KZK4 View 3D Structure Click here
I1JU88 View 3D Structure Click here
I1JW53 View 3D Structure Click here
I1K0T7 View 3D Structure Click here
I1KGV8 View 3D Structure Click here
I1KKP0 View 3D Structure Click here
I1KVJ5 View 3D Structure Click here
I1KZA2 View 3D Structure Click here
I1L2Q4 View 3D Structure Click here
I1L327 View 3D Structure Click here
I1LDM4 View 3D Structure Click here
I1M9F3 View 3D Structure Click here
I1MPJ0 View 3D Structure Click here
I1MWY0 View 3D Structure Click here
I1MXV1 View 3D Structure Click here
K7MLN3 View 3D Structure Click here
K7VMH6 View 3D Structure Click here
K7VT63 View 3D Structure Click here
O49393 View 3D Structure Click here
O81728 View 3D Structure Click here
Q0JB96 View 3D Structure Click here
Q10QF4 View 3D Structure Click here
Q10T56 View 3D Structure Click here
Q337L1 View 3D Structure Click here
Q4CQT6 View 3D Structure Click here
Q4D3X5 View 3D Structure Click here
Q4DFR6 View 3D Structure Click here
Q4DJ21 View 3D Structure Click here
Q4DM33 View 3D Structure Click here
Q4DNK1 View 3D Structure Click here
Q4DWK7 View 3D Structure Click here
Q4DWL2 View 3D Structure Click here
Q4E560 View 3D Structure Click here
Q4E565 View 3D Structure Click here
Q4KM30 View 3D Structure Click here
Q54CK2 View 3D Structure Click here
Q54T20 View 3D Structure Click here
Q5AJX5 View 3D Structure Click here
Q5XIT6 View 3D Structure Click here
Q5Z918 View 3D Structure Click here
Q6DC39 View 3D Structure Click here
Q6H6I0 View 3D Structure Click here
Q6ICB0 View 3D Structure Click here
Q6K3E0 View 3D Structure Click here
Q6NQ19 View 3D Structure Click here
Q6PC81 View 3D Structure Click here
Q7K2B1 View 3D Structure Click here
Q8I2W1 View 3D Structure Click here
Q8I5M9 View 3D Structure Click here
Q8IJX2 View 3D Structure Click here
Q8LN31 View 3D Structure Click here
Q8RXP3 View 3D Structure Click here
Q8X1T0 View 3D Structure Click here
Q93VG8 View 3D Structure Click here
Q9BSY9 View 3D Structure Click here
Q9CQT7 View 3D Structure Click here
Q9D291 View 3D Structure Click here
Q9LVS8 View 3D Structure Click here
Q9SAI9 View 3D Structure Click here
Q9SFT9 View 3D Structure Click here
Q9SZZ4 View 3D Structure Click here
Q9SZZ6 View 3D Structure Click here
Q9VWH2 View 3D Structure Click here