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15  structures 949  species 1  interaction 3556  sequences 31  architectures

Family: TarH (PF02203)

Summary: Tar ligand binding domain homologue

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This is the Wikipedia entry entitled "Aspartate receptor". More...

Aspartate receptor Edit Wikipedia article

Tar ligand binding domain homologue
Ligand binding domain aspartate receptor.png
Ribbon diagram of the S. typhimurium aspartate receptor ligand binding domain[1]
Identifiers
Symbol TarH
Pfam PF02203
InterPro IPR003122
SMART TarH
SCOP 1lih
SUPERFAMILY 1lih

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.[2] 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.[3]

[edit] References

  1. ^ 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
  2. ^ 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. 
  3. ^ 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. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=55484. 

This article incorporates text from the public domain Pfam and InterPro IPR003122


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Tar ligand binding domain homologue Provide feedback

No Pfam abstract.

Internal database links

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.

Gene Ontology

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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 4HB_MCP (CL0457), which has the following description:

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

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
(88)
Full
(3556)
Representative proteomes NCBI
(4206)
Meta
(102)
RP15
(59)
RP35
(179)
RP55
(344)
RP75
(528)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(88)
Full
(3556)
Representative proteomes NCBI
(4206)
Meta
(102)
RP15
(59)
RP35
(179)
RP55
(344)
RP75
(528)
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
(88)
Full
(3556)
Representative proteomes NCBI
(4206)
Meta
(102)
RP15
(59)
RP35
(179)
RP55
(344)
RP75
(528)
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.

Pfam alignments:

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: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Author: 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 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 22.7 22.7
Trusted cut-off 22.7 22.7
Noise cut-off 22.6 22.6
Model length: 171
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

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

TarH

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 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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