Summary: ATP-dependent Clp protease adaptor protein ClpS

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Wikipedia: ATP-dependent Clp protease adaptor protein ClpS
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This is the Wikipedia entry entitled "ATP-dependent Clp protease adaptor protein ClpS". More...

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ATP-dependent Clp protease adaptor protein ClpS Edit Wikipedia article

ClpS

clpns with fragments

Identifiers

Symbol

ClpS

1mbx / SUPFAM

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

ClpS is an N-recognin in the N-end rule pathway.^[1] ClpS interacts with protein substrates that have a bulky hydrophobic residue (leucine, phenylalanine, tyrosine, and tryptophan) at the N-terminus. The protein substrate is then degraded by the ClpAP protease.^[2]^[3]

In molecular biology, the ATP-dependent Clp protease adaptor protein ClpS is a bacterial protein. In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins.^[4]

ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands.^[5] The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet.

References

^ Varshavsky, Alexander (2011-08-01). "The N-end rule pathway and regulation by proteolysis". Protein Science. 20 (8): 1298â€“1345. doi:10.1002/pro.666. ISSN 1469-896X. PMC 3189519. PMID 21633985.
^ Tasaki T, Sriram SM, Park KS, Kwon YT (10 April 2012). "The N-end rule pathway". Annu Rev Biochem. 81: 261â€“289. doi:10.1146/annurev-biochem-051710-093308. PMC 3610525. PMID 22524314.
^ Erbse, A.; Schmidt, R.; Bornemann, T.; Schneider-Mergener, J.; Mogk, A.; Zahn, R.; Dougan, D. A.; Bukau, B. (2006). "ClpS is an essential component of the N-end rule pathway in Escherichia coli". Nature. 439 (7077): 753â€“756. doi:10.1038/nature04412. PMID 16467841.
^ Dougan DA, Reid BG, Horwich AL, Bukau B (March 2002). "ClpS, a substrate modulator of the ClpAP machine". Mol. Cell. 9 (3): 673â€“83. doi:10.1016/S1097-2765(02)00485-9. PMID 11931773.
^ Zeth K, Ravelli RB, Paal K, Cusack S, Bukau B, Dougan DA (December 2002). "Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA". Nat. Struct. Biol. 9 (12): 906â€“11. doi:10.1038/nsb869. PMID 12426582.

This article incorporates text from the public domain Pfam and InterPro: IPR003769

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.

ATP-dependent Clp protease adaptor protein ClpS Provide feedback

In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins [1].

Literature references

Dougan DA, Reid BG, Horwich AL, Bukau B; , Mol Cell 2002;9:673-683.: ClpS, a substrate modulator of the ClpAP machine. PUBMED:11931773 EPMC:11931773
Zeth K, Ravelli RB, Paal K, Cusack S, Bukau B, Dougan DA; , Nat Struct Biol 2002;9:906-911.: Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA. PUBMED:12426582 EPMC:12426582

External database links

SCOP:

1mbx

This tab holds annotation information from the InterPro database.

InterPro entry IPR003769

In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins [ PUBMED:11931773 ].

ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands [ PUBMED:12426582 ]. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Biological process

protein catabolic process (GO:0030163)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

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View options

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 (242)	Full (7734)	Representative proteomes				UniProt (29020)
	Seed (242)	Full (7734)	RP15 (1016)	RP35 (3516)	RP55 (7532)	RP75 (12630)	UniProt (29020)
Jalview	View	View	View	View	View	View	View
HTML	View
PP/heatmap	₁

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (242)	Full (7734)	Representative proteomes				UniProt (29020)
	Seed (242)	Full (7734)	RP15 (1016)	RP35 (3516)	RP55 (7532)	RP75 (12630)	UniProt (29020)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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 (242)	Full (7734)	Representative proteomes				UniProt (29020)
	Seed (242)	Full (7734)	RP15 (1016)	RP35 (3516)	RP55 (7532)	RP75 (12630)	UniProt (29020)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

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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:

COG2127

Previous IDs:

DUF174;

Type:

Family

Sequence Ontology:

SO:0100021

Author:

Mian N

, Bateman A

, Moxon SJ

Number in seed:

242

Number in full:

7734

Average length of the domain:

76.60 aa

Average identity of full alignment:

29 %

Average coverage of the sequence by the domain:

16.65 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.0	20.0
Trusted cut-off	20.0	20.0
Noise cut-off	19.9	19.9

Model length:

80

Family (HMM) version:

19

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Species distribution

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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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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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 ClpS domain has been found. There are 61 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.

Protein	Predicted structure	External Information
A0A0R0IJ84	View 3D Structure	Click here
A0A1D6KP76	View 3D Structure	Click here
A0A1D8PLP8	View 3D Structure	Click here
B4FRF7	View 3D Structure	Click here
B7ZDA3	View 3D Structure	Click here
C6T1Z0	View 3D Structure	Click here
C6T435	View 3D Structure	Click here
D4A9U6	View 3D Structure	Click here
F8W4R2	View 3D Structure	Click here
O13731	View 3D Structure	Click here
O70481	View 3D Structure	Click here
P0A8Q6	View 3D Structure	Click here
P91133	View 3D Structure	Click here
P9WPC1	View 3D Structure	Click here
Q6WKZ8	View 3D Structure	Click here
Q6ZAA3	View 3D Structure	Click here
Q8IEB2	View 3D Structure	Click here
Q8IWV7	View 3D Structure	Click here
Q8IWV8	View 3D Structure	Click here
Q9SX29	View 3D Structure	Click here
Q9VX91	View 3D Structure	Click here

Family: ClpS (PF02617)

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