Summary: Lon protease (S16) C-terminal proteolytic domain
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This is the Wikipedia entry entitled "Lon protease family". More...
Lon protease family Edit Wikipedia article
ATP-dependent protease La (LON) domain | |||||||||
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![]() crystal structure of n-terminal domain of e.coli lon protease | |||||||||
Identifiers | |||||||||
Symbol | LON | ||||||||
Pfam | PF02190 | ||||||||
Pfam clan | CL0178 | ||||||||
InterPro | IPR003111 | ||||||||
SMART | LON | ||||||||
MEROPS | S16 | ||||||||
SCOP2 | 1zbo / SCOPe / SUPFAM | ||||||||
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Lon protease (S16) C-terminal proteolytic domain | |||||||||
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Identifiers | |||||||||
Symbol | LON | ||||||||
Pfam | PF05362 | ||||||||
Pfam clan | CL0329 | ||||||||
InterPro | IPR008269 | ||||||||
MEROPS | S16 | ||||||||
SCOP2 | 1rr9 / SCOPe / SUPFAM | ||||||||
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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 SF). In the eukaryotes the majority of the Lon proteases are located in the mitochondrial matrix.[1][2] 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.[3]
References
- ^ Wang N, Gottesman S, Willingham MC, Gottesman MM, Maurizi MR (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. PMC 47959. PMID 8248235.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Barakat S, Pearce DA, Sherman F, Rapp WD (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.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Van Dyck L, Pearce DA, Sherman F (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.
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ignored (help)CS1 maint: multiple names: authors list (link)
External links
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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.
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.
Literature references
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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
SCOOP: | ChlI PDZ PDZ_2 PDZ_6 Peptidase_M50 |
Similarity to PfamA using HHSearch: | ChlI |
External database links
MEROPS: | S16 |
SCOP: | 1rr9 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR008269
Lon (also known as endopeptidase La) is a multi-domain ATP- dependent protease found throughout all kingdoms of life. It is involved in protein quality control and several regulatory processes. All Lon proteases contain an ATPase domain belonging to the AAA+ superfamily of molecular machines, and a proteolytic domain with a serine-lysine catalytic dyad in which a lysine assists the catalytic serine in proteolytic cleavage. Lon proteases can be divided into two subfamilies: A type (A-Lons), which have a large multi-lobed N-terminal domain together with the ATPase and protease domains, and B type (B-Lons), which lack an N domain, but have a membrane-anchoring region emerging from the ATPase domain. B-Lons are found in Archaea, in which they are the lone membrane-anchored ATP-dependent protease. The soluble A-Lons are found in all bacteria and in eukaryotic cell organelles, such as mitochondria and peroxisomes, and are needed for recovery from various stress conditions [ PUBMED:14665623 , PUBMED:15456757 , PUBMED:16002085 , PUBMED:20834233 , PUBMED:20222013 , PUBMED:24520911 ]. The Lon proteolytic domain forms peptidase family S16 of clan SJ [ PUBMED:16002085 ].
The structure of the Lon proteolytic domain consists of six alpha helices and ten beta strands [ PUBMED:14665623 , PUBMED:15456757 , PUBMED:16002085 , PUBMED:20834233 , PUBMED:20222013 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | serine-type endopeptidase activity (GO:0004252) |
ATP-dependent peptidase activity (GO:0004176) | |
Biological process | proteolysis (GO:0006508) |
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 S5 (CL0329), which has the following description:
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 18 members:
ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_NAlignments
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...
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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 (23) |
Full (17660) |
Representative proteomes | UniProt (79301) |
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RP15 (2917) |
RP35 (8949) |
RP55 (17547) |
RP75 (28489) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (23) |
Full (17660) |
Representative proteomes | UniProt (79301) |
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RP15 (2917) |
RP35 (8949) |
RP55 (17547) |
RP75 (28489) |
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Raw Stockholm | |||||||
Gzipped |
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.
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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
Seed source: | Merops |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Studholme DJ |
Number in seed: | 23 |
Number in full: | 17660 |
Average length of the domain: | 179.4 aa |
Average identity of full alignment: | 33 % |
Average coverage of the sequence by the domain: | 25.31 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 205 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 Lon_C domain has been found. There are 212 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.