LON

Found in ATP-dependent protease La (LON)

• SMART accession number: SM00464
• Description: N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs.
• Interpro abstract (IPR003111):

  In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:

  • Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
  • Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.

  In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.

  Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes [(PUBMED: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 [(PUBMED: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 [(PUBMED: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 [(PUBMED:7845208)]. The geometric orientations of the catalytic residues are similar between families, despite different protein folds [(PUBMED: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) [(PUBMED:7845208), (PUBMED:8439290)].

  This signature defines the N-terminal domain of the archael, bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). In the eukaryotes the majority of the proteins are located in the mitochondrial matrix [(PUBMED:8248235), (PUBMED:9620272)]. In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response [(PUBMED:8276800)].

• GO process: proteolysis (GO:0006508)
• GO function: ATP-dependent peptidase activity (GO:0004176)

There are 1513 LON domains in 1513 proteins in SMART's nrdb database.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
50.00	map00240	Pyrimidine metabolism
50.00	map00230	Purine metabolism

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with LON domain which could be assigned to a KEGG orthologous group, and not all proteins containing LON domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of LON domains in PDB

PDB code	Title
1zbo	X-ray crystal structure of protein bpp1347 from bordetella parapertussis. northeast structural genomics consortium target bor27.
2ane	Crystal structure of n-terminal domain of e.coli lon protease

Links (links to other resources describing this domain)

• INTERPRO: IPR003111
• PROSITE: LON_SER