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904  structures 912  species 12  interactions 8888  sequences 92  architectures

Family: Asp (PF00026)

Summary: Eukaryotic aspartyl protease

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Aspartate protease Edit Wikipedia article

Eukaryotic aspartyl protease
PDB 1lyb EBI.jpg
Structures of native and inhibited forms of human cathepsin D.[1]
Symbol Asp
Pfam PF00026
InterPro IPR001461
SCOP 1mpp
OPM superfamily 108
OPM protein 1lyb

Aspartic proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited by pepstatin.

Aspartic endopeptidases EC 3.4.23. of vertebrate, fungal and retroviral origin have been characterised.[2] More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin[3] and archaean preflagellin have been described.[4][5]

Eukaryotic aspartic proteases include pepsins, cathepsins, and renins. They have a two-domain structure, arising from ancestral duplication. Retroviral and retrotransposon proteases (Pfam PF00077) are much smaller and appear to be homologous to a single domain of the eukaryotic aspartyl proteases. Each domain contributes a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulfide bridges are other conserved features of aspartic peptidases.

Catalytic Mechanism

Proposed mechanism of peptide cleavage by aspartyl proteases.[6]

Aspartyl proteases are a highly specific family of proteases - they tend to cleave dipeptide bonds that have hydrophobic residues as well as a beta-methylene group. Unlike serine or cysteine proteases these proteases do not form a covalent intermediate during cleavage. Proteolysis therefore occurs in a single step.

While a number of different mechanisms for aspartyl proteases have been proposed, the most widely accepted is a general acid-base mechanism involving coordination of a water molecule between the two highly conserved aspartate residues.[6][7] One aspartate activates the water by abstracting a proton, enabling the water to perform a nucleophilic attack on the carbonyl carbon of the substrate scissile bond, generating a tetrahedral oxyanion intermediate. Rearrangement of this intermediate leads to protonation of the scissile amide which results in the splitting of the substrate peptide into two product peptides.


Pepstatin is an inhibitor of aspartate proteases.


All aspartate proteases have a highly conserved sequence of Asp-Thr-Gly. In general, with the exception of HIV - a dimer of two identical subunits - these enzymes are monomeric enzymes consisting of two, nearly-symmetrical domains. Because of this organisation, it is thought that these domains may have arisen through ancestral gene duplication.


There are six catalytic types of protease: aspartic acid, cysteine, glutamic acid, metallo, serine and threonine.

The aspartase proteases are divided into four families.

  • Family A01 (Pepsin family)
  • Family A02
  • Family A22
  • Family Ax1

A fifth family has also been described. This family is derived from the prolactin-induced protein/gross cystic disease fluid protein-15 (PIP/GCDFP15).


PDB 1htr EBI.jpg
crystal and molecular structures of human progastricsin at 1.62 angstroms resolution
Symbol A1_Propeptide
Pfam PF07966
InterPro IPR012848

Many eukaryotic aspartic endopeptidases (MEROPS peptidase family A1) are synthesised with signal and propeptides. The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide. The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residue in the propeptide. This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions.[8][9]



Human proteins containing this domain


Other organisms

External links

See also


  1. ^ Baldwin ET, Bhat TN, Gulnik S et al. (July 1993). "Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design". Proc. Natl. Acad. Sci. U.S.A. 90 (14): 6796–800. doi:10.1073/pnas.90.14.6796. PMC 47019. PMID 8393577. 
  2. ^ Szecsi PB (1992). "The aspartic proteases". Scand. J. Clin. Lab. In vest. Suppl. 210: 5–22. doi:10.3109/00365519209104650. PMID 1455179. 
  3. ^ Taylor R K, LaPointe CF (2000). "The type 4 prepilin peptidases comprise a novel family of aspartic acid proteases". J. Biol. Chem. 275 (2): 1502–10. doi:10.1074/jbc.275.2.1502. PMID 10625704. 
  4. ^ Jarrell KF, Ng SY, Chaban B (2006). "Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications". J. Mol. Microbiol. Bio technol. 11 (3): 167–91. doi:10.1159/000094053. PMID 16983194. 
  5. ^ Jarrell KF, Bardy SL (2003). "Cleavage of preflagellins by an aspartic acid signal peptidase is essential for flagellation in the archaeon Methanococcus voltae". Mol. Microbiol. 50 (4): 1339–1347. doi:10.1046/j.1365-2958.2003.03758.x. PMID 14622420. 
  6. ^ a b Suguna K, Padlan EA, Smith CW, Carlson WD, Davies DR (1987). "Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action". Proc. Natl. Acad. Sci. U.S.A. 84 (20): 7009–13. doi:10.1073/pnas.84.20.7009. PMC 299218. PMID 3313384. 
  7. ^ Brik A, Wong CH (2003). "HIV-1 protease: mechanism and drug discovery". Org. Biomol. Chem. 1 (1): 5–14. doi:10.1039/b208248a. PMID 12929379. 
  8. ^ Hartsuck JA, Koelsch G, Remington SJ (May 1992). "The high-resolution crystal structure of porcine pepsinogen". Proteins 13 (1): 1–25. doi:10.1002/prot.340130102. PMID 1594574. 
  9. ^ Sielecki AR, Fujinaga M, Read RJ, James MN (June 1991). "Refined structure of porcine pepsinogen at 1.8 A resolution". J. Mol. Biol. 219 (4): 671–92. doi:10.1016/0022-2836(91)90664-R. PMID 2056534. 

This article incorporates text from the public domain Pfam and InterPro IPR012848

This article incorporates text from the public domain Pfam and InterPro IPR000036

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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 IPR001461

Aspartic peptidase, also known as aspartyl proteases (EC) are a widely distributed family of proteolytic enzymes [PUBMED:6795036, PUBMED:2194475, PUBMED:1851433] known to exist in vertebrates, fungi, plants, retroviruses and some plant viruses. Aspartate proteases of eukaryotes are monomeric enzymes which consist of two domains. Each domain contains an active site centred on a catalytic aspartyl residue. The two domains most probably evolved from the duplication of an ancestral gene encoding a primordial domain. Currently known eukaryotic aspartyl proteases are:

  • Vertebrate gastric pepsins A and C (also known as gastricsin). Vertebrate chymosin (rennin), involved in digestion and used for making cheese.
  • Vertebrate lysosomal cathepsins D (EC and E (EC
  • Mammalian renin (EC whose function is to generate angiotensin I from angiotensinogen in the plasma.
  • Fungal proteases such as aspergillopepsin A (EC, candidapepsin (EC, mucoropepsin (EC (mucor rennin), endothiapepsin (EC, polyporopepsin (EC, and rhizopuspepsin (EC
  • Yeast saccharopepsin (EC (proteinase A) (gene PEP4). PEP4 is implicated in posttranslational regulation of vacuolar hydrolases.
  • Yeast barrierpepsin (EC (gene BAR1); a protease that cleaves alpha-factor and thus acts as an antagonist of the mating pheromone.
  • Fission yeast sxa1 which is involved in degrading or processing the mating pheromones.

Most retroviruses and some plant viruses, such as badnaviruses, encode for an aspartyl protease which is an homodimer of a chain of about 95 to 125 amino acids. In most retroviruses, the protease is encoded as a segment of a polyprotein which is cleaved during the maturation process of the virus. It is generally part of the pol polyprotein and, more rarely, of the gag polyprotein.

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_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_A2B Peptidase_A2E Peptidase_A3 RVP RVP_2 Spuma_A9PTase TAXi_C TAXi_N Zn_protease


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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
Author: Eddy SR, Griffiths-Jones SR, Finn RD
Number in seed: 23
Number in full: 8888
Average length of the domain: 285.60 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 69.49 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 80369284 -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: 317
Family (HMM) version: 19
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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


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There are 12 interactions for this family. More...

Serpin V-set Pepsin-I3 A1_Propeptide Serpin SapB_2 SH3_1 SapB_1 A1_Propeptide Asp Inhibitor_I34 SapB_2


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 904 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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