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Protein Domain : IPR001356

Name  Homeobox domain Short Name  Homeobox_dom
Type  Domain Description  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 [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. 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.

Publication Counts Displayer

2 Child Features

DB identifier Name Short Name Type
IPR020479 Homeodomain, metazoa Homeobox_metazoa Domain
IPR008422 Homeobox KN domain Homeobox_KN_domain Domain

2 Contains

DB identifier Name Short Name Type
IPR017970 Homeobox, conserved site Homeobox_CS Conserved_site
IPR000047 Helix-turn-helix motif HTH_motif Conserved_site

3 Cross References

Identifier
Source . Name

Subject . Primary Identifier
PF00046 PFAM IPR001356
PS50071 PROFILE IPR001356
SM00389 SMART IPR001356

3 Data Sets

Name URL
Swiss-Prot data set http://ca.expasy.org/sprot
InterPro data set  
InterPro GO Annotation data set  

10 Found In

DB identifier Name Short Name Type
IPR015584 POU domain-containing protein, class 4-related POU4-related Family
IPR016233 Homeobox protein Pitx/unc30 Homeobox_Pitx/unc30 Family
IPR016362 Transcription factor, homeobox/POU Transcription_factor_POU Family
IPR003022 Transcription factor Otx2 Otx2_TF Family
IPR003026 Transcription factor Otx1 Otx1_TF Family
IPR003025 Transcription factor Otx Otx_TF Family
IPR000972 Octamer-binding transcription factor TF_octamer Family
IPR015586 Pituitary-specific positive transcription factor 1 Pit_1 Family
IPR015585 POU domain-containing protein, class 5 POU_dom_5 Family
IPR017112 Homeobox protein Hox9 Homeobox_Hox9 Family

3 GO Annotation


Subject . Secondary Identifier

Subject . Name

Subject . Symbol

Ontology Term . Identifier

Ontology Term . Name
Homeobox domain   GO:0003700 sequence-specific DNA binding transcription factor activity
Homeobox domain   GO:0043565 sequence-specific DNA binding
Homeobox domain   GO:0006355 regulation of transcription, DNA-templated

3 Ontology Annotations


Subject . Secondary Identifier

Subject . Name

Subject . Symbol

Ontology Term . Identifier

Ontology Term . Name
Homeobox domain   GO:0003700 sequence-specific DNA binding transcription factor activity
Homeobox domain   GO:0043565 sequence-specific DNA binding
Homeobox domain   GO:0006355 regulation of transcription, DNA-templated

1 Parent Features

DB identifier Name Short Name Type
IPR009057 Homeodomain-like Homeodomain-like Domain

1222 Proteins

DB identifier Primary Accession
Organism . Name
FBpp0309366 Q9VWH1 Drosophila melanogaster
FBpp0081170 P09089 Drosophila melanogaster
FBpp0082796 D8FT40 Drosophila melanogaster
FBpp0082793 P83949 Drosophila melanogaster
FBpp0087053 A1Z916 Drosophila melanogaster
FBpp0087054 Q7JR08 Drosophila melanogaster
FBpp0099911 Q9W4B3 Drosophila melanogaster
FBpp0087175 P05527 Drosophila melanogaster
FBpp0089241 Q7KSY5 Drosophila melanogaster
FBpp0089244 Q7KSY6 Drosophila melanogaster
FBpp0089242 Q7KSY7 Drosophila melanogaster
FBpp0089245 P02833 Drosophila melanogaster
FBpp0309910 B7Z003 Drosophila melanogaster
FBpp0070105 P22808 Drosophila melanogaster
FBpp0110229 Q0KHX8 Drosophila melanogaster
FBpp0088920 Q04787 Drosophila melanogaster
FBpp0071889 Q9W1U7 Drosophila melanogaster
FBpp0082824 A4V304 Drosophila melanogaster
FBpp0082826 P09087 Drosophila melanogaster
FBpp0084461 P10181 Drosophila melanogaster
FBpp0079882 P06601 Drosophila melanogaster
FBpp0099525 Q9VTX7 Drosophila melanogaster
FBpp0099809 Q59DQ1 Drosophila melanogaster
FBpp0099810 Q59DQ2 Drosophila melanogaster
FBpp0077805 Q9VPL4 Drosophila melanogaster
FBpp0081139 P02835 Drosophila melanogaster
FBpp0083521 P22807 Drosophila melanogaster
FBpp0308955 A8Y527 Drosophila melanogaster
FBpp0112475 A8Y525 Drosophila melanogaster
FBpp0112474 Q7PL95 Drosophila melanogaster