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33  structures 1653  species 0  interactions 1666  sequences 4  architectures

Family: SspB (PF04386)

Summary: Stringent starvation protein B

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Stringent starvation protein B Provide feedback

Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA [1]. However, more recent work has cast doubt on the importance of SspB in wild-type cells [2]. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates [3].

Literature references

  1. Flynn JM, Levchenko I, Seidel M, Wickner SH, Sauer RT, Baker TA; , Proc Natl Acad Sci U S A 2001;98:10584-10589.: Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. PUBMED:11535833 EPMC:11535833

  2. Bohn C, Binet E, Bouloc P; , Mol Genet Genomics 2002;266:827-831.: Screening for stabilization of proteins with a trans-translation signature in Escherichia coli selects for inactivation of the ClpXP protease. PUBMED:11810257 EPMC:11810257

  3. Levchenko I, Seidel M, Sauer RT, Baker TA; , Science 2000;289:2354-2356.: A specificity-enhancing factor for the ClpXP degradation machine. PUBMED:11009422 EPMC:11009422


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007481

Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB is a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA [PUBMED:11535833]. However, more recent work has cast doubt on the importance of SspB in wild-type cells [PUBMED:11810257]. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates [PUBMED:11009422].

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 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
(137)
Full
(1666)
Representative proteomes NCBI
(1037)
Meta
(412)
RP15
(87)
RP35
(197)
RP55
(277)
RP75
(367)
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Format an alignment

  Seed
(137)
Full
(1666)
Representative proteomes NCBI
(1037)
Meta
(412)
RP15
(87)
RP35
(197)
RP55
(277)
RP75
(367)
Alignment:
Format:
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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
(137)
Full
(1666)
Representative proteomes NCBI
(1037)
Meta
(412)
RP15
(87)
RP35
(197)
RP55
(277)
RP75
(367)
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: COG2969
Previous IDs: none
Type: Family
Author: Kerrison ND
Number in seed: 137
Number in full: 1666
Average length of the domain: 152.90 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 95.39 %

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 20.0 20.0
Trusted cut-off 20.0 20.2
Noise cut-off 19.8 19.7
Model length: 155
Family (HMM) version: 8
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 SspB domain has been found. There are 33 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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