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13  structures 482  species 0  interactions 998  sequences 41  architectures

Family: Peptidase_C13 (PF01650)

Summary: Peptidase C13 family

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Peptidase C13 family Provide feedback

Members of this family are asparaginyl peptidases [1]. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation [2]. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterised as a 'haemoglobinase', but this term is probably incorrect [2]. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed [3].

Literature references

  1. Chen JM, Dando PM, Rawlings ND, Brown MA, Young NE, Stevens RA, Hewitt E, Watts C, Barrett AJ; , J Biol Chem 1997;272:8090-8098.: Cloning, isolation, and characterization of mammalian legumain, an asparaginyl endopeptidase. PUBMED:9065484 EPMC:9065484

  2. Caffrey CR, McKerrow JH, Salter JP, Sajid M; , Trends Parasitol 2004;20:241-248.: Blood 'n' guts: an update on schistosome digestive peptidases. PUBMED:15105025 EPMC:15105025

  3. Caffrey CR, Mathieu MA, Gaffney AM, Salter JP, Sajid M, Lucas KD, Franklin C, Bogyo M, McKerrow JH; , FEBS Lett 2000;466:244-248.: Identification of a cDNA encoding an active asparaginyl endopeptidase of Schistosoma mansoni and its expression in Pichia pastoris. PUBMED:10682836 EPMC:10682836


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001096

Asparaginyl endopeptidase, also known as legumain, is a family of cysteine proteases found in many organisms. This group of cysteine peptidases belong to the MEROPS peptidase family C13 (legumain family, clan CD). A type example is legumain from Canavalia ensiformis (Jack bean, Horse bean) [PUBMED:7852272]. Although legumains were first described from beans (also known as Vacuolar Processing Enzymes), homologues have been identified in plants, protozoa, vertebrates, and helminths [PUBMED:7845226, PUBMED:9065484]. In blood-feeding helminths, asparaginyl endopeptidases (sometimes described as hemoglobinases) have been located in the gut and are considered to be involved in host hemoglobin digestion [PUBMED:8457210, PUBMED:15275249, PUBMED:24696276, PUBMED:17028179].

Also included in the family C13 of cysteine peptidases are GPI-anchor transamidases, which share significant homology with legumains. GPI-anchor transamidases mediate glycosylphosphatidylinositol (GPI) anchoring in the endoplasmic reticulum [PUBMED:8978684, PUBMED:10793132].

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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Pfam Clan

This family is a member of clan Peptidase_CD (CL0093), which has the following description:

The members of this clan are all endopeptidase that have the catalytic dyad histidine followed by cysteine. The catalytic histidine is preceded by a block of hydrophobic residues and a glycine, where as the cysteine is preceded by a block of hydrophobic residues and a glutamine and an alanine. The members with a know structure adopt an alpha/beta fold [1].

The clan contains the following 8 members:

CHAT Peptidase_C11 Peptidase_C13 Peptidase_C14 Peptidase_C25 Peptidase_C50 Peptidase_C80 Raptor_N

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(34)
Full
(998)
Representative proteomes UniProt
(2969)
NCBI
(3796)
Meta
(50)
RP15
(341)
RP35
(650)
RP55
(892)
RP75
(1072)
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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
(34)
Full
(998)
Representative proteomes UniProt
(2969)
NCBI
(3796)
Meta
(50)
RP15
(341)
RP35
(650)
RP55
(892)
RP75
(1072)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(34)
Full
(998)
Representative proteomes UniProt
(2969)
NCBI
(3796)
Meta
(50)
RP15
(341)
RP35
(650)
RP55
(892)
RP75
(1072)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: Pfam-B_1302 (release 4.1)
Previous IDs: none
Type: Family
Author: Bateman A, Caffrey C
Number in seed: 34
Number in full: 998
Average length of the domain: 226.80 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 54.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.4 20.4
Trusted cut-off 20.4 20.5
Noise cut-off 20.3 20.1
Model length: 256
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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_C13 domain has been found. There are 13 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 seqence.

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