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33  structures 477  species 0  interactions 1680  sequences 54  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

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This is the Wikipedia entry entitled "Methyl-accepting chemotaxis proteins". More...

Methyl-accepting chemotaxis proteins Edit Wikipedia article

MCPsignal
3zx6.png
Methyl-accepting chemotaxis protein I. PDB entry 3zx6[1]
Identifiers
SymbolMCPsignal
PfamPF00015
Pfam clanCL0510
InterProIPR004089
PROSITEPDOC00465
SCOP21qu7 / SCOPe / SUPFAM
CDDcd11386
Methyl-accepting chemotaxis proteins
Ligand binding domain aspartate receptor.png
Ribbon diagram of the S. typhimurium aspartate receptor ligand binding domain[2]
Identifiers
SymbolMethyl-accepting chemotaxis proteins (MCP)
PfamPF02203
InterProIPR004090
SMARTTarH
SCOP21lih / SCOPe / SUPFAM
CDDcd00181

The Methyl-accepting chemotaxis proteins (MCP, also aspartate receptor) are a family of transmembrane receptors that mediate chemotactic response in certain enteric bacteria, such as Salmonella typhimurium and Escherichia coli.[3] 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. Use of the MCP allows bacteria to detect concentrations of molecules in the extracellular matrix so that the bacteria may smooth swim or tumble accordingly. If the bacterium detects rising levels of attractants (nutrients) or declining levels of repellents (toxins), the bacterium will continue swimming forward, or smooth swimming. If the bacterium detects declining levels of attractants or rising levels of repellents, the bacterium will tumble and re-orient itself in a new direction. In this manner, a bacterium may swim towards nutrients and away from toxins[4]

Evolution

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.[5]

Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs.[6] 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).

Structure

MCPs share similar structure and signalling mechanism. MCPs form dimers. Three dimers of MCP spontaneously form trimers. Trimers are complexed by CheA and CheW into hexagonal lattices. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. Most MCPs contain: (a) an N-terminal signal peptide that is a transmembrane alpha-helix in the mature protein; (b) a poorly-conserved periplasmic receptor (ligand-binding) domain; (c) a transmembrane alpha-helix; (d) generally one or more HAMP domains and (e) a highly conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the methylated glutamate residues.

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.

Function

Binding a ligand causes a conformational change in the MCP receptor which translates down the hairpin structure and inhibits its sensor kinase. At the tip of the hairpin are two proteins that associate to the MCP: CheW and CheA. CheA acts as the sensor kinase. CheA has kinase activity and autophosphorylates itself on a histidyl residue when activated by the MCP. CheW is believed to be a transducer of the signal from the MCP to CheA. Activated CheA transfers its phosphoryl group to CheY, a response regulator. Phosphorylated CheY phosphorylates the basal body FliM which is connected to the flagellum. Phosphorylation of the basal body acts as a flagellar switch and changes the direction of rotation of the flagellum. This change in direction allows for alternation between smooth swimming and tumbling which biases the bacterial random walk towards attractant.


References

  1. ^ Ferris, H. U.; Zeth, K.; Hulko, M.; Dunin-Horkawicz, S.; Lupas, A. N. (2014). "Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. Coli serine chemoreceptor". Journal of Structural Biology. 186 (3): 349–356. doi:10.1016/j.jsb.2014.03.015. PMID 24680785.
  2. ^ PDB: 1VLT​; Yeh JI, Biemann HP, Privé GG, Pandit J, Koshland DE Jr, Kim SH (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.; rendered with PyMOL
  3. ^ 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.
  4. ^ Derr P, Boder E, Goulian M (February 2006). "Changing the specificity of a bacterial chemoreceptor". J. Mol. Biol. 355 (5): 923–32. doi:10.1016/j.jmb.2005.11.025. PMID 16359703.
  5. ^ 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. Bibcode:2001PNAS...98.9517Y. doi:10.1073/pnas.161239298. PMC 55484. PMID 11504940.
  6. ^ Alexander RP, Zhulin IB (February 2007). "Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors". Proc. Natl. Acad. Sci. U.S.A. 104 (8): 2885–90. doi:10.1073/pnas.0609359104. PMC 1797150. PMID 17299051.
This article incorporates text from the public domain Pfam and InterPro: IPR004089
This article incorporates text from the public domain Pfam and InterPro: IPR003122

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.

Tar ligand binding domain homologue Provide feedback

This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors, such as E.coli Tar (taxis to aspartate and repellents), which is a receptor for the attractant L-aspartate [1,2] and also recognises proteogenic amino acids, phthalic acid, Malic acid, 3,4-dihydroxymandelic acid, citrate, benzoate and derivatives, protocatechuate, vanillate, quinate, shikimate and dehydroshikimate (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

Literature references

  1. Milburn MV, Prive GG, Milligan DL, Scott WG, Yeh J, Jancarik J, Koshland DE Jr, Kim SH;, Science. 1991;254:1342-1347.: Three-dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand. PUBMED:1660187 EPMC:1660187

  2. Mise T;, Biochemistry. 2016;55:3708-3713.: Structural Analysis of the Ligand-Binding Domain of the Aspartate Receptor Tar from Escherichia coli. PUBMED:27292793 EPMC:27292793


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, such as E.coli Tar (taxis to aspartate and repellents), which is a receptor for the attractant L-aspartate [ PUBMED:1660187 , PUBMED:27292793 ]. It is a homodimeric receptor that contains an N-terminal periplasmic ligand binding domain, a transmembrane region, a HAMP domain and a C-terminal cytosolic signaling domain [ PUBMED:21689529 ].

Gene Ontology

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Domain organisation

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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 4 members:

4HB_MCP_1 CHASE3 HBM TarH

Alignments

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  Seed
(67)
Full
(1680)
Representative proteomes UniProt
(16678)
RP15
(79)
RP35
(447)
RP55
(1647)
RP75
(4623)
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  Seed
(67)
Full
(1680)
Representative proteomes UniProt
(16678)
RP15
(79)
RP35
(447)
RP55
(1647)
RP75
(4623)
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  Seed
(67)
Full
(1680)
Representative proteomes UniProt
(16678)
RP15
(79)
RP35
(447)
RP55
(1647)
RP75
(4623)
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Trees

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Curation and family details

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Curation View help on the curation process

Seed source: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: SMART
Number in seed: 67
Number in full: 1680
Average length of the domain: 169.50 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 30.83 %

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 25.2 23.0
Trusted cut-off 25.2 23.5
Noise cut-off 25.1 22.9
Model length: 177
Family (HMM) version: 18
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 TarH 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 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
P02941 View 3D Structure Click here
P02942 View 3D Structure Click here
P05704 View 3D Structure Click here
P07017 View 3D Structure Click here
P07018 View 3D Structure Click here
Q02755 View 3D Structure Click here