Active Site

Peptidase S16, active site (IPR008268)

Short name: Peptidase_S16_AS


Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [PMID: 7845208]. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence [PMID: 7845208]. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [PMID: 7845208].

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base [PMID: 7845208]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds [PMID: 7845208]. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [PMID: 7845208, PMID: 8439290].

This signature defines the active site of the serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). These proteases which are dependent on the hydrolysis of ATP for their activity and have a serine in their active site, they include:

  • Bacterial ATP-dependent proteases [PMID: 8294008, PMID: 8331083]. The prototype of those bacterial enzymes is the Escherichia coli La protease (EC: (gene lon). La is capable of hydrolysing large proteins; it degrades short-lived regulatory (such as rcsA and sulA) and abnormal proteins. It is a cytoplasmic protein of 87 kDa that associates as an homotetramer. Its proteolytic activity is stimulated by single-stranded DNA.
  • Eukaryotic mitochondrial matrix proteases [PMID: 8276800, PMID: 8248235]. The prototype of these enzymes is the yeast PIM1 protease. It is a mitochondrial matrix protein of 120 kDa that associated as an homohexamer. It catalyses the initial step of mitochondrial protein degradation.
  • Haemophilus influenzae lon-B (HI1324), a protein which does not contain the ATP-binding domain, but possess a slightly divergent form of the catalytic domain.

GO terms

Biological Process

GO:0006508 proteolysis

Molecular Function

GO:0004176 ATP-dependent peptidase activity
GO:0004252 serine-type endopeptidase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE patterns