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1924  structures 1566  species 0  interactions 24251  sequences 398  architectures

Family: Asp (PF00026)

Summary: Eukaryotic aspartyl protease

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

This is the Wikipedia entry entitled "Aspartate protease". More...

Aspartate protease Edit Wikipedia article

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This is the Wikipedia entry entitled "Aspartic protease". More...

Aspartic protease Edit Wikipedia article

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This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

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

External database links

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_protease

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
(24)
Full
(24251)
Representative proteomes UniProt
(40652)
RP15
(5235)
RP35
(12120)
RP55
(19051)
RP75
(24960)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(24)
Full
(24251)
Representative proteomes UniProt
(40652)
RP15
(5235)
RP35
(12120)
RP55
(19051)
RP75
(24960)
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
(24)
Full
(24251)
Representative proteomes UniProt
(40652)
RP15
(5235)
RP35
(12120)
RP55
(19051)
RP75
(24960)
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: Overington enriched
Previous IDs: asp;
Type: Family
Sequence Ontology: SO:0100021
Author: Eddy SR , Griffiths-Jones SR , Finn RD
Number in seed: 24
Number in full: 24251
Average length of the domain: 284.2 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 68.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.9 19.9
Trusted cut-off 19.9 19.9
Noise cut-off 19.8 19.8
Model length: 315
Family (HMM) version: 26
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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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Asp domain has been found. There are 1924 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
A0A044RC12 View 3D Structure Click here
A0A044UMJ9 View 3D Structure Click here
A0A044UMM5 View 3D Structure Click here
A0A077Z4E5 View 3D Structure Click here
A0A077Z943 View 3D Structure Click here
A0A077ZAI4 View 3D Structure Click here
A0A077ZC41 View 3D Structure Click here
A0A0D2DW80 View 3D Structure Click here
A0A0D2E8F7 View 3D Structure Click here
A0A0D2EKG0 View 3D Structure Click here
A0A0D2ENZ9 View 3D Structure Click here
A0A0D2F0Q5 View 3D Structure Click here
A0A0D2F6U0 View 3D Structure Click here
A0A0D2G225 View 3D Structure Click here
A0A0D2G600 View 3D Structure Click here
A0A0D2G6U2 View 3D Structure Click here
A0A0D2GB97 View 3D Structure Click here
A0A0D2GEW2 View 3D Structure Click here
A0A0D2GNQ6 View 3D Structure Click here
A0A0D2GNT4 View 3D Structure Click here
A0A0D2GQ32 View 3D Structure Click here
A0A0D2GW38 View 3D Structure Click here
A0A0G2KH37 View 3D Structure Click here
A0A0K0DWM8 View 3D Structure Click here
A0A0K0DWM9 View 3D Structure Click here
A0A0K0DWN0 View 3D Structure Click here
A0A0K0DWN1 View 3D Structure Click here
A0A0K0E1Q1 View 3D Structure Click here
A0A0K0E9F8 View 3D Structure Click here
A0A0K0EAR6 View 3D Structure Click here
A0A0K0EBE1 View 3D Structure Click here
A0A0K0ENN2 View 3D Structure Click here
A0A0K0EPI8 View 3D Structure Click here
A0A0K0EQD6 View 3D Structure Click here
A0A0K0JSJ6 View 3D Structure Click here
A0A0N4UMP9 View 3D Structure Click here
A0A0P0V5L9 View 3D Structure Click here
A0A0P0X4Z4 View 3D Structure Click here
A0A0P0XDT2 View 3D Structure Click here
A0A0P0XUU5 View 3D Structure Click here