Summary: Eukaryotic aspartyl protease
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Eukaryotic aspartyl protease Provide feedback
Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (PF00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.
Internal database links
SCOOP: | Asp_protease_2 gag-asp_proteas SapB_1 SapB_2 TAXi_C TAXi_N |
Similarity to PfamA using HHSearch: | TAXi_C TAXi_N |
External database links
HOMSTRAD: | asp |
MEROPS: | A1 |
PRINTS: | PR00792 |
PROSITE: | PDOC00128 |
SCOP: | 1mpp |
This tab holds annotation information from the InterPro database.
InterPro entry IPR033121
Aspartyl proteases (APs), also known as acid proteases, ([intenz:3.4.23.-]) are a widely distributed family of proteolytic enzymes [PUBMED:6795036, PUBMED:2194475, PUBMED:1851433, PUBMED:15771507, PUBMED:24869856, PUBMED:1455179] known to exist in vertebrates, fungi, plants, retroviruses and some plant viruses. APs use an Asp dyad to hydrolyze peptide bonds.
APs found in eukaryotic cells are alpha/beta monomers composed of two asymmetric lobes ("bilobed"). Each of the lobes provides a catalytic Asp residue, positioned within the hallmark motif Asp-Thr/Ser-Gly, to the active site. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbour hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. Eukaryotic APs form peptidase family A1 of clan AA.
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_AA (CL0129), which has the following description:
This clan contains aspartic peptidases, including the pepsins and retropepsins. These enzymes contains a catalytic dyad composed of two aspartates. In the retropepsins one is provided by each copy of a homodimeric protein, whereas in the pepsin-like peptidases these aspartates come from a single protein composed of two duplicated domains.
The clan contains the following 14 members:
Asp Asp_protease Asp_protease_2 DUF1758 gag-asp_proteas Peptidase_A2_2 Peptidase_A2B Peptidase_A3 RVP RVP_2 Spuma_A9PTase TAXi_C TAXi_N Zn_proteaseAlignments
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 (24) |
Full (17622) |
Representative proteomes | UniProt (30664) |
NCBI (54185) |
Meta (72) |
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RP15 (3221) |
RP35 (8585) |
RP55 (13196) |
RP75 (18155) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (24) |
Full (17622) |
Representative proteomes | UniProt (30664) |
NCBI (54185) |
Meta (72) |
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RP15 (3221) |
RP35 (8585) |
RP55 (13196) |
RP75 (18155) |
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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.
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
Seed source: | Overington enriched |
Previous IDs: | asp; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Eddy SR |
Number in seed: | 24 |
Number in full: | 17622 |
Average length of the domain: | 290.20 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 68.54 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 315 | ||||||||||||
Family (HMM) version: | 24 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
There are 12 interactions for this family. More...
SapB_2 Inhibitor_I34 Asp SH3_1 SapB_2 A1_Propeptide Serpin SapB_1 A1_Propeptide Serpin V-set Pepsin-I3Structures
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 Asp domain has been found. There are 1571 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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