Summary: Lon protease (S16) C-terminal proteolytic domain
This is the Wikipedia entry entitled "Lon protease family". More...
Does Pfam agree with the content of the Wikipedia entry ?
Editing Wikipedia articles
Before you edit for the first time
You should take a few minutes to view the following pages:
How your contribution will be recorded
Lon protease family Edit Wikipedia article
||This article may be too technical for most readers to understand. (February 2012)|
|ATP-dependent protease La (LON) domain|
crystal structure of n-terminal domain of e.coli lon protease
|Lon protease (S16) C-terminal proteolytic domain|
In molecular biology, the Lon protease family is a family of proteases. They are found in archaea, bacteria and eukaryotes. Lon proteases are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ). In the eukaryotes the majority of the Lon proteases are located in the mitochondrial matrix. In yeast, the Lon protease PIM1 is located in the mitochondrial matrix. It is required for mitochondrial function, it is constitutively expressed but is increased after thermal stress, suggesting that PIM1 may play a role in the heat shock response.
- Wang N, Gottesman S, Willingham MC, Gottesman MM, Maurizi MR (December 1993). "A human mitochondrial ATP-dependent protease that is highly homologous to bacterial Lon protease". Proc. Natl. Acad. Sci. U.S.A. 90 (23): 11247–51. doi:10.1073/pnas.90.23.11247. PMC 47959. PMID 8248235.
- Barakat S, Pearce DA, Sherman F, Rapp WD (May 1998). "Maize contains a Lon protease gene that can partially complement a yeast pim1-deletion mutant". Plant Mol. Biol. 37 (1): 141–54. PMID 9620272.
- Van Dyck L, Pearce DA, Sherman F (January 1994). "PIM1 encodes a mitochondrial ATP-dependent protease that is required for mitochondrial function in the yeast Saccharomyces cerevisiae". J. Biol. Chem. 269 (1): 238–42. PMID 8276800.
Lon protease (S16) C-terminal proteolytic domain Provide feedback
The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.
Vasilyeva OV, Kolygo KB, Leonova YF, Potapenko NA, Ovchinnikova TV; , FEBS Lett 2002;526:66-70.: Domain structure and ATP-induced conformational changes in Escherichia coli protease Lon revealed by limited proteolysis and autolysis. PUBMED:12208506 EPMC:12208506
Internal database links
|Similarity to PfamA using HHSearch:||ChlI|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR008269
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 C-terminal proteolytic domain of the archael, bacterial and eukaryotic Lon proteases, which are ATP-dependent serine peptidases belonging to peptidase family S16 (Lon protease family, clan SF).
|Molecular function||serine-type endopeptidase activity (GO:0004252)|
|ATP-dependent peptidase activity (GO:0004176)|
|Biological process||proteolysis (GO:0006508)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.
The clan contains the following 14 members:ChlI DNA_mis_repair EFG_IV Fae GHMP_kinases_N IGPD Lon_C LpxC Ribonuclease_P Ribosomal_S5_C RNase_PH Topo-VIb_trans UPF0029 Xol-1_N
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||25|
|Number in full:||7706|
|Average length of the domain:||174.80 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||25.91 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Lon_C domain has been found. There are 58 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.
Loading structure mapping...