Summary: Tar ligand binding domain homologue
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|Tar ligand binding domain homologue|
Ribbon diagram of the S. typhimurium aspartate receptor ligand binding domain
The aspartate receptor, Tar, is a member of a family of transmembrane receptors that mediate chemotactic response in certain enteric bacteria, such as Salmonella typhimurium and Escherichia coli. These methyl-accepting chemotaxis receptors are one of the first components in the sensory excitation and adaptation responses in bacteria, which act to alter swimming behaviour upon detection of specific chemicals. The aspartate receptor mediates movement towards the attractants aspartate and maltose, and away from the repellents nickel and cobalt. There are many different types of bacterial 60 kDa transmembrane receptors, which share similar topology and signalling mechanisms. They possess three domains: a periplasmic ligand-binding domain, two transmembrane segments, and a cytoplasmic domain. The structure of the ligand-binding domain comprises a closed or partly opened, four-helical bundle with a left-handed twist. The difference in the sequence of the ligand-binding domain between receptors reflects the different ligand specificities. Binding of the ligand causes a conformational change that is transmitted across the membrane to the cytoplasmic activation domain.
- PDB 1VLT; Yeh JI, Biemann HP, Privé GG, Pandit J, Koshland DE Jr, and Kim SH (1996). "High-resolution structures of the ligand binding domain of the wild-type bacterial aspartate receptor". J Mol Biol 262: 186–201. doi:10.1006/jmbi.1996.0507. PMID 8831788.; rendered with PyMOL
- Kim SH, Prive GG, Pandit J, Koshland DE, Yeh JI, Biemann HP (1996). "High-resolution structures of the ligand binding domain of the wild-type bacterial aspartate receptor". J. Mol. Biol. 262 (2): 186–201. doi:10.1006/jmbi.1996.0507. PMID 8831788.
- Koshland DE, Yu EW (2001). "Propagating conformational changes over long (and short) distances in proteins". Proc. Natl. Acad. Sci. U.S.A. 98 (17): 9517–9520. doi:10.1073/pnas.161239298. PMC 55484. PMID 11504940.
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Tar ligand binding domain homologue Provide feedback
No Pfam abstract.
Internal database links
|Similarity to PfamA using HHSearch:||4HB_MCP_1|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003122
Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour [PUBMED:16359703]. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs [PUBMED:17299051]. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides).
MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues.
This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Molecular function||transmembrane signaling receptor activity (GO:0004888)|
|Biological process||signal transduction (GO:0007165)|
- the number of sequences which exhibit this architecture
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This superfamily is characterised by a four-helix bundle structure that forms a ubiquitous sensory module in prokaryotic signal-transduction. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors.
The clan contains the following 3 members:4HB_MCP_1 CHASE3 TarH
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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Curation and family details
|Seed source:||Alignment kindly provided by SMART|
|Number in seed:||88|
|Number in full:||3556|
|Average length of the domain:||164.70 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||30.56 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 TarH domain has been found. There are 15 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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