SMART: Pfam domain HARE-HTH

The domain within your query sequence starts at position 11 and ends at position 83; the E-value for the HARE-HTH domain shown below is 3.6e-22.

RTWAEAAKTVLEKYPNTPMSHKEILQVIQREGLKEIRCGTSPLACLNAMLHTNSRGEEGI
FYKVPGRMGVYTL

HARE-HTH

PFAM accession number:	PF05066
Interpro abstract (IPR007759):	The Asx-like (Asxl) proteins includes Asxl1-3. They are putative Polycomb group (PcG) proteins, which act by forming multiprotein complexes that are required to maintain the transcriptionally repressive state of homeotic genes throughout development. Asxl1 is involved in transcriptional regulation mediated by ligand-bound retinoic acid receptors (RARs) and peroxisome proliferator-activated receptor gamma (PPARG) [ (PUBMED:16606617) ]. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling [ (PUBMED:10336502) ]. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [ (PUBMED:7545758) ]. It participates in both the initiation and recycling phases of transcription. This domain, known as the HARE-HTH domain, adopts the winged helix-turn-helix fold and is predicted to bind DNA. It can be found at the N terminus of the ASXL protein. It can also be found in several other eukaryotic chromatin proteins (such as HB1 in plants), diverse restriction endonucleases and DNA glycosylases, the RNA polymerase delta subunit of Gram-positive bacteria and certain bacterial proteins that combine features of the RNA polymerase alpha-subunit and sigma factors [ (PUBMED:22186017) ]. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC [ (PUBMED:10336502) ]. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors [ (PUBMED:10336502) ]. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein [ (PUBMED:7545758) (PUBMED:22186017) ].
GO process:	regulation of transcription, DNA-templated (GO:0006355), transcription, DNA-templated (GO:0006351)

PFAM accession number:

PF05066

Interpro abstract (IPR007759):

The Asx-like (Asxl) proteins includes Asxl1-3. They are putative Polycomb group (PcG) proteins, which act by forming multiprotein complexes that are required to maintain the transcriptionally repressive state of homeotic genes throughout development. Asxl1 is involved in transcriptional regulation mediated by ligand-bound retinoic acid receptors (RARs) and peroxisome proliferator-activated receptor gamma (PPARG) [ (PUBMED:16606617) ].

The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling [ (PUBMED:10336502) ]. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [ (PUBMED:7545758) ]. It participates in both the initiation and recycling phases of transcription.

This domain, known as the HARE-HTH domain, adopts the winged helix-turn-helix fold and is predicted to bind DNA. It can be found at the N terminus of the ASXL protein. It can also be found in several other eukaryotic chromatin proteins (such as HB1 in plants), diverse restriction endonucleases and DNA glycosylases, the RNA polymerase delta subunit of Gram-positive bacteria and certain bacterial proteins that combine features of the RNA polymerase alpha-subunit and sigma factors [ (PUBMED:22186017) ]. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC [ (PUBMED:10336502) ]. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors [ (PUBMED:10336502) ]. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein [ (PUBMED:7545758) (PUBMED:22186017) ].

GO process:

regulation of transcription, DNA-templated (GO:0006355), transcription, DNA-templated (GO:0006351)

This is a PFAM domain. For full annotation and more information, please see the PFAM entry HARE-HTH