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1874  structures 1475  species 0  interactions 22739  sequences 392  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 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
(22739)
Representative proteomes UniProt
(43519)
RP15
(4888)
RP35
(11257)
RP55
(17973)
RP75
(23513)
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
(22739)
Representative proteomes UniProt
(43519)
RP15
(4888)
RP35
(11257)
RP55
(17973)
RP75
(23513)
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
(24)
Full
(22739)
Representative proteomes UniProt
(43519)
RP15
(4888)
RP35
(11257)
RP55
(17973)
RP75
(23513)
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: 22739
Average length of the domain: 283.70 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 67.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -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: 25
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 Asp domain has been found. There are 1874 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
A0A0G2KH37 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
A0A0R0E9Y9 View 3D Structure Click here
A0A0R0EVR0 View 3D Structure Click here
A0A0R0FFL6 View 3D Structure Click here
A0A0R0GA69 View 3D Structure Click here
A0A0R0H5M6 View 3D Structure Click here
A0A0R0H5M6 View 3D Structure Click here
A0A0R0H7D5 View 3D Structure Click here
A0A0R0H7D5 View 3D Structure Click here
A0A0R0KLL5 View 3D Structure Click here
A0A0R4INF8 View 3D Structure Click here
A0A144A171 View 3D Structure Click here
A0A1D6E6I1 View 3D Structure Click here
A0A1D6F9P6 View 3D Structure Click here
A0A1D6FAT4 View 3D Structure Click here
A0A1D6FKF4 View 3D Structure Click here
A0A1D6GEA7 View 3D Structure Click here
A0A1D6GPB0 View 3D Structure Click here
A0A1D6GSX3 View 3D Structure Click here
A0A1D6H629 View 3D Structure Click here
A0A1D6HAE9 View 3D Structure Click here
A0A1D6IFM3 View 3D Structure Click here
A0A1D6INV1 View 3D Structure Click here
A0A1D6IXZ0 View 3D Structure Click here
A0A1D6KKS4 View 3D Structure Click here
A0A1D6KTR8 View 3D Structure Click here
A0A1D6KTV3 View 3D Structure Click here
A0A1D6L3M2 View 3D Structure Click here
A0A1D6LB85 View 3D Structure Click here
A0A1D6LHL0 View 3D Structure Click here
A0A1D6LYS4 View 3D Structure Click here
A0A1D6M2V9 View 3D Structure Click here
A0A1D6NI08 View 3D Structure Click here
A0A1D6NTJ5 View 3D Structure Click here
A0A1D6NVV5 View 3D Structure Click here
A0A1D6Q423 View 3D Structure Click here
A0A1D8PG34 View 3D Structure Click here
A0A1D8PGX5 View 3D Structure Click here
A0A1D8PGZ9 View 3D Structure Click here
A1Z9Q9 View 3D Structure Click here
B7ZWD6 View 3D Structure Click here
C0P3K6 View 3D Structure Click here
C0P7L5 View 3D Structure Click here
F1QDA2 View 3D Structure Click here
F4JKD9 View 3D Structure Click here
G3V8C5 View 3D Structure Click here
G5EC01 View 3D Structure Click here
G5EEI4 View 3D Structure Click here
I1KNG0 View 3D Structure Click here
I1KZU7 View 3D Structure Click here
I1L1Y7 View 3D Structure Click here
I1LAZ3 View 3D Structure Click here
I1LYD2 View 3D Structure Click here
I1MHN2 View 3D Structure Click here
I1MS12 View 3D Structure Click here
I1NBM7 View 3D Structure Click here
I1NEU4 View 3D Structure Click here
K7KGI6 View 3D Structure Click here
K7V6R3 View 3D Structure Click here
O01530 View 3D Structure Click here
O01531 View 3D Structure Click here
O01532 View 3D Structure Click here
O09043 View 3D Structure Click here
O16338 View 3D Structure Click here
O16339 View 3D Structure Click here
O45072 View 3D Structure Click here
O59774 View 3D Structure Click here
O65390 View 3D Structure Click here
O76856 View 3D Structure Click here
O77350 View 3D Structure Click here
O96009 View 3D Structure Click here
P00796 View 3D Structure Click here
P00797 View 3D Structure Click here
P04073 View 3D Structure Click here
P06281 View 3D Structure Click here
P07267 View 3D Structure Click here
P07339 View 3D Structure Click here
P08424 View 3D Structure Click here
P0CY27 View 3D Structure Click here
P0CY29 View 3D Structure Click here
P0DJ06 View 3D Structure Click here
P0DJD7 View 3D Structure Click here
P0DJD8 View 3D Structure Click here
P0DJD9 View 3D Structure Click here
P12630 View 3D Structure Click here
P14091 View 3D Structure Click here
P16228 View 3D Structure Click here
P18242 View 3D Structure Click here
P20142 View 3D Structure Click here
P24268 View 3D Structure Click here
P32329 View 3D Structure Click here
P32834 View 3D Structure Click here
P40583 View 3D Structure Click here
P42211 View 3D Structure Click here
P43094 View 3D Structure Click here
P53057 View 3D Structure Click here
P53379 View 3D Structure Click here
P55956 View 3D Structure Click here
P56817 View 3D Structure Click here
P56818 View 3D Structure Click here
P56819 View 3D Structure Click here
P70269 View 3D Structure Click here
Q06325 View 3D Structure Click here
Q0JKM8 View 3D Structure Click here
Q12303 View 3D Structure Click here
Q18020 View 3D Structure Click here
Q1L9E4 View 3D Structure Click here
Q21966 View 3D Structure Click here
Q22972 View 3D Structure Click here
Q3E740 View 3D Structure Click here
Q42456 View 3D Structure Click here
Q54CE2 View 3D Structure Click here
Q54WT3 View 3D Structure Click here
Q55CH2 View 3D Structure Click here
Q59SU1 View 3D Structure Click here
Q59SU1 View 3D Structure Click here
Q59U59 View 3D Structure Click here
Q59VH7 View 3D Structure Click here
Q5A651 View 3D Structure Click here
Q5A8N2 View 3D Structure Click here
Q5AC08 View 3D Structure Click here
Q5AEM6 View 3D Structure Click here
Q5AH56 View 3D Structure Click here
Q5XJ89 View 3D Structure Click here
Q6IE75 View 3D Structure Click here
Q6XQJ0 View 3D Structure Click here
Q7JKL9 View 3D Structure Click here
Q7K485 View 3D Structure Click here
Q86KL6 View 3D Structure Click here
Q86NE0 View 3D Structure Click here
Q8I6V3 View 3D Structure Click here
Q8I6Z5 View 3D Structure Click here
Q8IAS0 View 3D Structure Click here
Q8IJ71 View 3D Structure Click here
Q8IKI0 View 3D Structure Click here
Q8ILG2 View 3D Structure Click here
Q8ILG2 View 3D Structure Click here
Q8IM15 View 3D Structure Click here
Q8IM16 View 3D Structure Click here
Q8MYN5 View 3D Structure Click here
Q8MYN6 View 3D Structure Click here
Q8MYN7 View 3D Structure Click here
Q8VYL3 View 3D Structure Click here
Q94271 View 3D Structure Click here
Q9D106 View 3D Structure Click here
Q9D7R7 View 3D Structure Click here
Q9JJX2 View 3D Structure Click here
Q9JL18 View 3D Structure Click here
Q9LGZ3 View 3D Structure Click here
Q9LQA9 View 3D Structure Click here
Q9QX71 View 3D Structure Click here
Q9VEK3 View 3D Structure Click here
Q9VEK4 View 3D Structure Click here
Q9VEK5 View 3D Structure Click here
Q9VKP6 View 3D Structure Click here
Q9VKP7 View 3D Structure Click here
Q9VLK3 View 3D Structure Click here
Q9VQ11 View 3D Structure Click here
Q9VQ12 View 3D Structure Click here
Q9VQ13 View 3D Structure Click here
Q9VQ14 View 3D Structure Click here
Q9W5G3 View 3D Structure Click here
Q9XEC4 View 3D Structure Click here
Q9Y5Z0 View 3D Structure Click here