SMART accession number:SM00389
Description: DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Interpro abstract (IPR001356): The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [(PUBMED:2568852), (PUBMED:1357790), ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [(PUBMED:12445403)]. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure.

The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.

GO process:regulation of transcription, DNA-templated (GO:0006355)
GO function:sequence-specific DNA binding (GO:0043565), sequence-specific DNA binding transcription factor activity (GO:0003700)
Family alignment:
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There are 44025 HOX domains in 38753 proteins in SMART's nrdb database.

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