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553  structures 20266  species 1  interaction 38696  sequences 36  architectures

Family: CLP_protease (PF00574)

Summary: Clp protease

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "CLP protease family". More...

CLP protease family Edit Wikipedia article

CLP_protease
PDB 2f6i EBI.jpg
crystal structure of the clpp protease catalytic domain from plasmodium falciparum
Identifiers
Symbol CLP_protease
Pfam PF00574
Pfam clan CL0127
InterPro IPR001907
PROSITE PDOC00358
MEROPS S14
SCOP 1tyf
SUPERFAMILY 1tyf
CDD cd00394

In molecular biology, the CLP protease family is a family of serine peptidases belong to the MEROPS peptidase family S14 (ClpP endopeptidase family, clan SK). ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin.[1] It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP,[1] although the P subunit alone does possess some catalytic activity.

Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity.

References[edit]

  1. ^ a b Maurizi MR, Clark WP, Katayama Y, Rudikoff S, Pumphrey J, Bowers B, Gottesman S (July 1990). "Sequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli". J. Biol. Chem. 265 (21): 12536–45. PMID 2197275. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR001907

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.

Clp protease Provide feedback

The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. P48254 has lost all of these active site residues and is therefore inactive. P42379 contains two large insertions, P42380 contains one large insertion.

Literature references

  1. Wang J, Hartling JA, Flanagan JM; , Cell 1997;91:447-456.: The structure of ClpP at 2.3 angstroms resolution suggests a model for ATP-dependent proteolysis. PUBMED:9390554 EPMC:9390554


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR023562

This entry includes peptidases from the MEROPS peptidase family S14, including ClpP endopeptidase and translocation-enhancing protein TepA.

ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin [PUBMED:2197275]. It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP [PUBMED:2197275], although the P subunit alone does possess some catalytic activity. Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity.

Translocation-enhancing protein TepA displays sequence similarity to ClpP. It is required for efficient translocation of pre-proteins across the membrane [PUBMED:10455123].

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 ClpP_crotonase (CL0127), which has the following description:

This family includes several peptidases of peptidase clan SK as well as crotonase like proteins.

The clan contains the following 10 members:

ACCA Carboxyl_trans CLP_protease ECH_1 ECH_2 MdcE Peptidase_S41 Peptidase_S49 Peptidase_S49_N SDH_sah

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(68)
Full
(38696)
Representative proteomes NCBI
(18408)
Meta
(4575)
RP15
(761)
RP35
(1935)
RP55
(2717)
RP75
(3408)
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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
(68)
Full
(38696)
Representative proteomes NCBI
(18408)
Meta
(4575)
RP15
(761)
RP35
(1935)
RP55
(2717)
RP75
(3408)
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
(68)
Full
(38696)
Representative proteomes NCBI
(18408)
Meta
(4575)
RP15
(761)
RP35
(1935)
RP55
(2717)
RP75
(3408)
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.

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: Prosite
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 68
Number in full: 38696
Average length of the domain: 175.10 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 73.66 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.1 20.1
Model length: 182
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

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

CLP_protease

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 CLP_protease domain has been found. There are 553 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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