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44  structures 2301  species 0  interactions 3630  sequences 7  architectures

Family: CsrA (PF02599)

Summary: Global regulator protein family

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This is the Wikipedia entry entitled "CsrA protein". More...

CsrA protein Edit Wikipedia article

CsrA
PDB 1y00 EBI.png
CsrA dimer from Escherichia coli.[1]
Identifiers
SymbolCsrA
PfamPF02599
InterProIPR003751

Carbon storage regulator A (CsrA) is a RNA binding protein. The CsrA homologs are found in most bacterial species, in the pseudomonads they are called repressor of secondary metabolites (RsmA and RsmE). The CsrA proteins generally bind to the Shine-Dalgarno sequence of messenger RNAs and either inhibit translation or facilitate mRNA decay.[2]

CsrA has a regulatory effect on glycogen biosynthesis and catabolism, glycolysis and

Interactions

The CsrA protein binds to a Stem-loop RNA motif. The ability of the protein to inhibit translation of bound mRNAs is inhibit by the expression of sRNA such as CsrB, CsrC, RsmZ, RsmY and RsmX that contain multiple copies of the RNA motif. These RNAs sequester CsrA, which allows the translation of the previously inhibited bound mRNAs.

An example of an RNA stem-loop

References

  1. ^ Gutiérrez, P; Li, Y; Osborne, MJ; Pomerantseva, E; Liu, Q; Gehring, K (2005 May). "Solution structure of the carbon storage regulator protein CsrA from Escherichia coli". Journal of bacteriology. 187 (10): 3496–501. PMID 15866937. {{cite journal}}: Check date values in: |date= (help)
  2. ^ Liu, MY; Gui, G; Wei, B; Preston JF, 3rd; Oakford, L; Yüksel, U; Giedroc, DP; Romeo, T (1997 Jul 11). "The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli". The Journal of biological chemistry. 272 (28): 17502–10. PMID 9211896. {{cite journal}}: Check date values in: |date= (help)

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.

Global regulator protein family Provide feedback

This is a family of global regulator proteins. This protein is a RNA-binding protein and a global regulator of carbohydrate metabolism genes facilitating mRNA decay [1]. In E. coli CsrA binds the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [1]. In other bacteria such as Erwinia caratovara RmsA has been shown to regulate the production of virulence determinants, such extracellular enzymes [2]. RmsA binds to RmsB regulatory RNA.

Literature references

  1. Liu MY, Gui G, Wei B, Preston JF 3rd, Oakford L, Yuksel U, Giedroc DP, Romeo T; , J Biol Chem 1997;272:17502-17510.: The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. PUBMED:9211896 EPMC:9211896

  2. Cui Y, Chatterjee A, Liu Y, Dumenyo CK, Chatterjee AK; , J Bacteriol 1995;177:5108-5115.: Identification of a global repressor gene, rsmA, of Erwinia carotovora subsp. carotovora that controls extracellular enzymes, N-(3-oxohexanoyl)-L-homoserine lactone, and pathogenicity in soft-rotting Erwinia spp. PUBMED:7665490 EPMC:7665490


This tab holds annotation information from the InterPro database.

InterPro entry IPR003751

The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay [ PUBMED:9211896 ]. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [ PUBMED:9211896 ].

Gene Ontology

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

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...

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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
(244)
Full
(3630)
Representative proteomes UniProt
(17849)
RP15
(705)
RP35
(2080)
RP55
(3727)
RP75
(6511)
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  Seed
(244)
Full
(3630)
Representative proteomes UniProt
(17849)
RP15
(705)
RP35
(2080)
RP55
(3727)
RP75
(6511)
Alignment:
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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
(244)
Full
(3630)
Representative proteomes UniProt
(17849)
RP15
(705)
RP35
(2080)
RP55
(3727)
RP75
(6511)
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.

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: COG1551
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 244
Number in full: 3630
Average length of the domain: 52.7 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 68.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.1
Noise cut-off 26.9 26.9
Model length: 53
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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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 CsrA domain has been found. There are 44 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
A0A0H3GWL4 View 3D Structure Click here
A0KPF9 View 3D Structure Click here
A0LC90 View 3D Structure Click here
A0PZZ6 View 3D Structure Click here
A1S4F1 View 3D Structure Click here
A1SER2 View 3D Structure Click here
A1SZZ9 View 3D Structure Click here
A1WXK3 View 3D Structure Click here
A3DHL2 View 3D Structure Click here
A3N017 View 3D Structure Click here
A3QC90 View 3D Structure Click here
A4J774 View 3D Structure Click here
A4VJB5 View 3D Structure Click here
A4XWE0 View 3D Structure Click here
A5EWA3 View 3D Structure Click here
A5G8X2 View 3D Structure Click here
A5I5H1 View 3D Structure Click here
A5MZ33 View 3D Structure Click here
A6TCV8 View 3D Structure Click here
A6TL88 View 3D Structure Click here
A6VKD5 View 3D Structure Click here
A7HN71 View 3D Structure Click here
A8ANQ0 View 3D Structure Click here
A8F501 View 3D Structure Click here
A8FHX3 View 3D Structure Click here
A8H1T7 View 3D Structure Click here
A8MJP4 View 3D Structure Click here
A9IE54 View 3D Structure Click here
A9KSQ2 View 3D Structure Click here
A9MFZ2 View 3D Structure Click here
B0SQM8 View 3D Structure Click here
B0UTE2 View 3D Structure Click here
B1KPS4 View 3D Structure Click here
B1YLK2 View 3D Structure Click here
B2A826 View 3D Structure Click here
B2FL34 View 3D Structure Click here
B2VHD3 View 3D Structure Click here
B3PCZ8 View 3D Structure Click here
B4EUV8 View 3D Structure Click here
B7GKZ6 View 3D Structure Click here