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58  structures 4472  species 1  interaction 7706  sequences 39  architectures

Family: Lon_C (PF05362)

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
PDB 2ane EBI.jpg
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
SCOP 1zbo
SUPERFAMILY 1zbo
Lon protease (S16) C-terminal proteolytic domain
Identifiers
Symbol LON
Pfam PF05362
Pfam clan CL0329
InterPro IPR008269
MEROPS S16
SCOP 1rr9
SUPERFAMILY 1rr9

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[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR003111

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

  1. 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

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).

Gene Ontology

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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

Alignments

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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
(25)
Full
(7706)
Representative proteomes NCBI
(8849)
Meta
(3459)
RP15
(804)
RP35
(1468)
RP55
(1899)
RP75
(2231)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(25)
Full
(7706)
Representative proteomes NCBI
(8849)
Meta
(3459)
RP15
(804)
RP35
(1468)
RP55
(1899)
RP75
(2231)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(25)
Full
(7706)
Representative proteomes NCBI
(8849)
Meta
(3459)
RP15
(804)
RP35
(1468)
RP55
(1899)
RP75
(2231)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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.

Note: You can also download the data file for the tree.

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: Merops
Previous IDs: none
Type: Domain
Author: Studholme DJ
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 205
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Lon_C

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 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.

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