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33  structures 5102  species 0  interactions 42435  sequences 1090  architectures

Family: HisKA_3 (PF07730)

Summary: Histidine kinase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Two-component regulatory system". More...

Two-component regulatory system Edit Wikipedia article

Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions.[1] They consist of a membrane-bound histidine kinase that senses a specific environmental stimulus and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes.[2]

References

  1. ^ Stock AM, Robinson VL, Goudreau PN (2000). "Two-component signal transduction". Annu. Rev. Biochem. 69: 183–215. doi:10.1146/annurev.biochem.69.1.183. PMID 10966457.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ Mascher T, Helmann JD, Unden G (2006). "Stimulus perception in bacterial signal-transducing histidine kinases". Microbiol. Mol. Biol. Rev. 70 (4): 910–38. doi:10.1128/MMBR.00020-06. PMID 17158704.{{cite journal}}: CS1 maint: multiple names: authors list (link)

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.

Histidine kinase Provide feedback

This is the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with PF00512 and PF07536.

Literature references

  1. Grebe TW, Stock JB; , Adv Microb Physiol 1999;41:139-227.: The histidine protein kinase superfamily. PUBMED:10500846 EPMC:10500846


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011712

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 ].

Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [ PUBMED:8868347 , PUBMED:11406410 ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [ PUBMED:10426948 ], and CheA, which plays a central role in the chemotaxis system [ PUBMED:9989504 ]. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water [ PUBMED:11145881 ]. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily.

HKs can be roughly divided into two classes: orthodox and hybrid kinases [ PUBMED:8029829 , PUBMED:1482126 ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK [ PUBMED:10966457 ]. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain.

This entry represetns the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with INTERPRO and INTERPRO .

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 His_Kinase_A (CL0025), which has the following description:

This is the dimerisation and phospho-acceptor domain of a sub-family of histidine kinases. It shares sequence similarity with Pfam:PF00512 and Pfam:PF07536. It is usually found adjacent to a C-terminal ATPase domain (Pfam:PF02518). This domain is found in a wide range of Bacteria and also several Archaea. It comprises one of the fundamental units of the two-component signal transduction system [2-7].

The clan contains the following 11 members:

H-kinase_dim HATPase_c HATPase_c_2 HATPase_c_3 HATPase_c_4 HATPase_c_5 HisKA HisKA_2 HisKA_3 HPTransfase HWE_HK

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...

View options

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
(163)
Full
(42435)
Representative proteomes UniProt
(164797)
RP15
(2813)
RP35
(17487)
RP55
(46326)
RP75
(80332)
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HTML View             
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
(163)
Full
(42435)
Representative proteomes UniProt
(164797)
RP15
(2813)
RP35
(17487)
RP55
(46326)
RP75
(80332)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(163)
Full
(42435)
Representative proteomes UniProt
(164797)
RP15
(2813)
RP35
(17487)
RP55
(46326)
RP75
(80332)
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: BLAST
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Studholme DJ
Number in seed: 163
Number in full: 42435
Average length of the domain: 67.4 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 14.69 %

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 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 68
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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 HisKA_3 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
A0A077Z6F6 View 3D Structure Click here
A0A0H3GPN7 View 3D Structure Click here
A0A0H3GV46 View 3D Structure Click here
G3XD66 View 3D Structure Click here
K0EMG8 View 3D Structure Click here
K0EN27 View 3D Structure Click here
K0EPF4 View 3D Structure Click here
K0EPN1 View 3D Structure Click here
K0ERU7 View 3D Structure Click here
K0ESA0 View 3D Structure Click here
K0ESL1 View 3D Structure Click here
K0ESV1 View 3D Structure Click here
K0EU20 View 3D Structure Click here
K0EUF1 View 3D Structure Click here
K0EUI8 View 3D Structure Click here
K0EVN4 View 3D Structure Click here
K0EWE5 View 3D Structure Click here
K0EWL5 View 3D Structure Click here
K0EXA0 View 3D Structure Click here
K0EXH3 View 3D Structure Click here
K0EXP6 View 3D Structure Click here
K0EYK1 View 3D Structure Click here
K0EZ23 View 3D Structure Click here
K0EZC3 View 3D Structure Click here
K0EZM8 View 3D Structure Click here
K0EZY6 View 3D Structure Click here
K0F168 View 3D Structure Click here
K0F1H6 View 3D Structure Click here
K0F1M1 View 3D Structure Click here
K0F2R9 View 3D Structure Click here
K0F3Q0 View 3D Structure Click here
K0F3Y0 View 3D Structure Click here
K0F475 View 3D Structure Click here
K0F4S0 View 3D Structure Click here
K0F4T5 View 3D Structure Click here
K0F5A2 View 3D Structure Click here
K0F5I7 View 3D Structure Click here
O07527 View 3D Structure Click here
O32198 View 3D Structure Click here
O34757 View 3D Structure Click here