Member database | PRINTS |
PRINTS type | domain |
Short name | HOMEOBOX |
Description Imported from IPR020479
This entry represents the homeodomain (HD), a protein domain of approximately 60 residues that usually binds DNA. It is encoded by the homeobox sequence
[3, 4], which 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
[2, 1]. Proteins containing HDs are likely to play an important role in development - most are known to be sequence-specific DNA-binding transcription factors. This domain folds into a globular structure with three α-helices connected by two short loops that harbour a hydrophobic core. The second and third form a helix-turn-helix (HTH) motif, which make intimate contacts with the DNA: while the first helix of this motif helps to stabilise the structure, 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
[3, 4]. One particularity of the HTH motif in some of these proteins arises from the stereo-chemical requirement for glycine in the turn (position 9 of the motif), which is needed to avoid steric interference of the β-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.
References Imported from IPR020479
1.The homeobox in perspective. Gehring WJ. Trends Biochem. Sci. 17, 277-80, (1992). View articlePMID: 1357790
2.The structure and function of the homeodomain. Scott MP, Tamkun JW, Hartzell GW 3rd. Biochim. Biophys. Acta 989, 25-48, (1989). View articlePMID: 2568852
3.Homeodomain proteins: an update. Burglin TR, Affolter M. Chromosoma 125, 497-521, (2016). PMID: 26464018
4.Classification and nomenclature of all human homeobox genes. Holland PW, Booth HA, Bruford EA. BMC Biol 5, 47, (2007). View articlePMID: 17963489
Further reading
5. A comprehensive classification and evolutionary analysis of plant homeobox genes. Mukherjee K, Brocchieri L, Burglin TR. Mol. Biol. Evol. 26, 2775-94, (2009). View articlePMID: 19734295
Supplementary References
Integrated to
Representative structure
3a03: Crystal structure of Hox11L1 homeodomain