InterPro : IPR009057

Name  Homeodomain-like Short Name  Homeodomain-like
Type  Domain Description  Homeodomain proteins are transcription factors that share a related DNA binding homeodomain []. The 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. 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. Many proteins contain homeodomains, including Drosophila Engrailed, yeast mating type proteins, hepatocyte nuclear factor 1a and HOX proteins.The homeodomain motif is very similar in sequence and structure to domains in a wide range of DNA-binding proteins, including recombinases, Myb proteins, GARP response regulators, human telomeric proteins (hTRF1), paired domain proteins (PAX), yeast RAP1, centromere-binding proteins CENP-B and ABP-1, transcriptional regulators (TyrR), AraC-type transcriptional activators, and tetracycline repressor-like proteins (TetR, QacR, YcdC) [, , ].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



17 Child Features

Id Name Short Name Type
IPR006600 HTH CenpB-type DNA-binding domain HTH_CenpB_DNA-bd_dom Domain
IPR001356 Homeobox domain Homeobox_dom Domain
IPR007889 DNA binding HTH domain, Psq-type HTH_Psq Domain
IPR023082 Homeo-prospero domain Homeo_prospero_dom Domain
IPR007526 SWIRM domain SWIRM Domain
IPR001005 SANT/Myb domain SANT/Myb Domain
IPR015195 SLIDE domain SLIDE Domain
IPR006120 Resolvase, HTH domain Resolvase_HTH_dom Domain
IPR002622 Transposase, Synechocystis PCC 6803 Transposase_14 Domain
IPR002197 DNA binding HTH domain, Fis-type HTH_Fis Domain
IPR025246 Transposase IS30-like HTH domain IS30-like_HTH Domain
IPR018060 DNA binding HTH domain, AraC-type HTH_AraC Domain
IPR001647 DNA-binding HTH domain, TetR-type HTH_TetR Domain
IPR015010 Rap1 Myb domain Rap1_Myb_dom Domain
IPR006455 Homeodomain, ZF-HD class Homeodomain_ZF_HD Domain
IPR014875 Mor transcription activator Mor_transcription_activator Domain
IPR024978 Homeodomain, phBC6A51-type Homeodomain_phBC6A51-type Domain

7 Contains

Id Name Short Name Type
IPR017970 Homeobox, conserved site Homeobox_CS Conserved_site
IPR000047 Helix-turn-helix motif HTH_motif Conserved_site
IPR020479 Homeodomain, metazoa Homeobox_metazoa Domain
IPR019737 Homeobox engrailed-type, conserved site Homoebox-engrailed_CS Conserved_site
IPR017930 Myb domain Myb_dom Domain
IPR015126 Mu DNA binding, I gamma subdomain Mu_I-gamma Domain
IPR015280 Rap1, DNA-binding domain Rap1_DNA-bd Domain

16 Found In

Id Name Short Name Type
IPR002514 Transposase IS3/IS911family Transposase_8 Family
IPR003220 InsA N-terminal domain InsA_N_dom Domain
IPR016233 Homeobox protein Pitx/unc30 Homeobox_Pitx/unc30 Family
IPR010113 Nif-specific regulatory protein Nif-specific_regulatory_prot Family
IPR012704 Signal transduction response regulator, propionate catabolism, transcriptional regulator PrpR Sig_transdc_resp-reg_PrpR Family
IPR005412 DNA-binding protein Fis Fis_DNA-bd Family
IPR014317 Transcription activator PspF Transcription_activator_PspF Family
IPR010114 Signal transduction response regulator, nitrogen regulation NR(I) Sig_transdc_resp-reg_NtrC Family
IPR014264 Signal transduction response regulator, PEP-CTERM system, putative Sig_transdc_resp-reg_PEP-CTERM Family
IPR011785 Transcription regulator PpsR Tscrpt_reg_PpsR-CrtJ Family
IPR000972 Octamer-binding transcription factor TF_octamer Family
IPR017894 HTH domain, IS21 transposase-type HTH_IS21_transposase_type Domain
IPR019915 Transcription regulator, pyrimidine utilisation, RutR Tscrpt_reg_pyr_util_RutR Family
IPR003022 Transcription factor Otx2 Otx2_TF Family
IPR003025 Transcription factor Otx Otx_TF Family
IPR003026 Transcription factor Otx1 Otx1_TF Family

0 Parent Features

4 Publications

First Author Title Year Journal Volume Pages
Kisker C The complex formed between Tet repressor and tetracycline-Mg2+ reveals mechanism of antibiotic resistance. 1995 J Mol Biol 247 260-80
Mannervik M Target genes of homeodomain proteins. 1999 Bioessays 21 267-70
Hosoda K Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators. 2002 Plant Cell 14 2015-29
Nishikawa T Solution structure of the DNA-binding domain of human telomeric protein, hTRF1. 1998 Structure 6 1057-65

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)