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790  structures 8295  species 0  interactions 391374  sequences 9932  architectures

Family: Response_reg (PF00072)

Summary: Response regulator receiver domain

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Response regulator receiver domain Provide feedback

This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.

Literature references

  1. Pao GM, Saier MH; , J Mol Evol 1995;40:136-154.: Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. PUBMED:7699720 EPMC:7699720


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001789

Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions [ PUBMED:16176121 ]. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk [ PUBMED:18076326 ]. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more [ PUBMED:12372152 ]. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) [ PUBMED:10966457 ]. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.

A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [ PUBMED:11934609 , PUBMED:11489844 ].

Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes [ PUBMED:7699720 ]. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others [ PUBMED:12015152 ]. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response [ PUBMED:10966457 ]. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained.

The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.

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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Pfam Clan

This family is a member of clan CheY (CL0304), which has the following description:

This clan includes the CheY-like response regulators from bacteria [1-2].

The clan contains the following 11 members:

cREC_REC FleQ NARF OKR_DC_1_N RcsC RcsD_ABL Response_reg Response_reg_2 TadZ_N UPF0004 VpsR

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
(52)
Full
(391374)
Representative proteomes UniProt
(1766993)
RP15
(47801)
RP35
(188590)
RP55
(406863)
RP75
(715567)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(52)
Full
(391374)
Representative proteomes UniProt
(1766993)
RP15
(47801)
RP35
(188590)
RP55
(406863)
RP75
(715567)
Alignment:
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Sequence:
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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
(52)
Full
(391374)
Representative proteomes UniProt
(1766993)
RP15
(47801)
RP35
(188590)
RP55
(406863)
RP75
(715567)
Raw Stockholm Download     Download   Download        
Gzipped 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: Prodom
Previous IDs: response_reg;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Griffiths-Jones SR , Finn RD , Fenech M
Number in seed: 52
Number in full: 391374
Average length of the domain: 112.30 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 29.26 %

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 30.2 30.2
Trusted cut-off 30.2 30.2
Noise cut-off 30.1 30.1
Model length: 112
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 Response_reg domain has been found. There are 790 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
A0A0P0XZB5 View 3D Structure Click here
A0A0R0E422 View 3D Structure Click here
A0A0R0EI42 View 3D Structure Click here
A0A0R0ENQ9 View 3D Structure Click here
A0A0R0EUY3 View 3D Structure Click here
A0A0R0G3R5 View 3D Structure Click here
A0A0R0GJ59 View 3D Structure Click here
A0A0R0GRK7 View 3D Structure Click here
A0A0R0HRH5 View 3D Structure Click here
A0A0R0IRI5 View 3D Structure Click here
A0A0R0JGD4 View 3D Structure Click here
A0A0R0JLN5 View 3D Structure Click here
A0A0R0JU68 View 3D Structure Click here
A0A0R0K0Q6 View 3D Structure Click here
A0A0R0K0S8 View 3D Structure Click here
A0A0R0KCZ8 View 3D Structure Click here
A0A0R0KVT4 View 3D Structure Click here
A0A0R0LKY2 View 3D Structure Click here
A0A1D6E9X4 View 3D Structure Click here
A0A1D6EDG3 View 3D Structure Click here
A0A1D6EF02 View 3D Structure Click here
A0A1D6EF25 View 3D Structure Click here
A0A1D6ETT5 View 3D Structure Click here
A0A1D6F525 View 3D Structure Click here
A0A1D6FHD1 View 3D Structure Click here
A0A1D6G5R1 View 3D Structure Click here
A0A1D6G6S9 View 3D Structure Click here
A0A1D6GEQ7 View 3D Structure Click here
A0A1D6GJ22 View 3D Structure Click here
A0A1D6GRV4 View 3D Structure Click here
A0A1D6HD83 View 3D Structure Click here
A0A1D6HN97 View 3D Structure Click here
A0A1D6I9R1 View 3D Structure Click here
A0A1D6J4G3 View 3D Structure Click here
A0A1D6JU17 View 3D Structure Click here
A0A1D6KQE2 View 3D Structure Click here
A0A1D6KTY7 View 3D Structure Click here
A0A1D6L285 View 3D Structure Click here
A0A1D6L3N2 View 3D Structure Click here
A0A1D6LJ19 View 3D Structure Click here