InterPro : IPR011991

Name  Winged helix-turn-helix DNA-binding domain Short Name  WHTH_DNA-bd_dom
Type  Domain Description  Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions.Many different proteins with diverse biological functions contain a winged helix DNA-binding domain, including transcriptional repressors such as biotin repressor, LexA repressor and the arginine repressor []; transcription factors such as the hepatocyte nuclear factor-3 proteins involved in cell differentiation, heat-shock transcription factor, and the general transcription factors TFIIE and TFIIF [, ]; helicases such as RuvB that promotes branch migration at the Holliday junction, and CDC6 in the pre-replication complex [, ]; endonucleases such as FokI and TnsA []; histones; and Mu transposase, where the flexible wing of the enhancer-binding domain is essential for efficient transposition [].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



36 Child Features

Id Name Short Name Type
IPR006630 RNA-binding protein Lupus La Lupus_La_RNA-bd Domain
IPR019559 Cullin protein, neddylation domain Cullin_neddylation_domain Domain
IPR000418 Ets domain Ets_dom Domain
IPR001346 Interferon regulatory factor DNA-binding domain Interferon_reg_fact_DNA-bd_dom Domain
IPR001766 Transcription factor, fork head TF_fork_head Domain
IPR005818 Linker histone H1/H5, domain H15 Histone_H1/H5_H15 Domain
IPR000591 DEP domain DEP_dom Domain
IPR003150 DNA-binding RFX-type winged-helix domain DNA-bd_RFX Domain
IPR000232 Heat shock factor (HSF)-type, DNA-binding HSF_DNA-bd Domain
IPR003316 E2F/DP family, winged-helix DNA-binding domain E2F_WHTH_DNA-bd_dom Domain
IPR015163 CDC6, C-terminal domain Cdc6_C_dom Domain
IPR020900 Arginine repressor, DNA-binding domain Arg_repress_DNA-bd Domain
IPR013196 Helix-turn-helix, type 11 HTH_11 Domain
IPR001845 HTH ArsR-type DNA-binding domain HTH_ArsR_DNA-bd_dom Domain
IPR000524 Transcription regulator HTH, GntR Tscrpt_reg_HTH_GntR Domain
IPR000847 Transcription regulator HTH, LysR Tscrpt_reg_HTH_LysR Domain
IPR016032 Signal transduction response regulator, C-terminal effector Sig_transdc_resp-reg_C-effctor Domain
IPR022687 Iron dependent repressor, N-terminal Fe_dep_repressor_HTH_DtxR_N Domain
IPR000835 MarR-type HTH domain HTH_MarR-typ Domain
IPR000485 AsnC-type HTH domain AsnC-type_HTH_dom Domain
IPR000607 Double-stranded RNA-specific adenosine deaminase (DRADA) dsRNA_A_deaminase Domain
IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding MethylDNA_cys_MeTrfase_DNA-bd Domain
IPR008823 DNA helicase, Holliday junction RuvB type, C-terminal DNA_helicase_Holl-junc_RuvB_C Domain
IPR015191 Translation elongation factor SelB, winged helix, type 3 Elong_fac_SelB-wing-hlx_typ-3 Domain
IPR004409 Biotin operon repressor, helix-turn-helix domain Biotin_operon_repress_HTH Domain
IPR005104 Winged helix-turn-helix transcription repressor, HrcA DNA-binding domain WHTH_HrcA_DNA-bd Domain
IPR002577 Helix-turn-helix, HxlR type HTH_HxlR Domain
IPR014793 Dissimilatory sulphite reductase D DsrD Domain
IPR005561 ANTAR domain ANTAR Domain
IPR002831 Transcription regulator TrmB, N-terminal Tscrpt_reg_TrmB_N Domain

15 Contains

Id Name Short Name Type
IPR013324 RNA polymerase sigma factor, region 3/4 RNA_pol_sigma_r3_r4 Domain
IPR018122 Transcription factor, fork head, conserved site TF_fork_head_CS Conserved_site
IPR016157 Cullin, conserved site Cullin_CS Conserved_site
IPR013196 Helix-turn-helix, type 11 HTH_11 Domain
IPR019817 Interferon regulatory factor, conserved site Interferon_reg_fac_CS Conserved_site
IPR001867 Signal transduction response regulator, C-terminal Sig_transdc_resp-reg_C Domain
IPR018334 ArsR-type transcription regulator, HTH motif ArsR_HTH Conserved_site
IPR017919 Transcription factor TFE/TFIIEalpha HTH domain TFIIE/TFIIEa_HTH Domain
IPR001808 Transcription regulator HTH, Crp Tscrpt_reg_HTH_Crp Domain
IPR001497 Methylated-DNA-[protein]-cysteine S-methyltransferase, active site MethylDNA_cys_MeTrfase_AS Active_site
IPR007630 RNA polymerase sigma-70 region 4 RNA_pol_sigma70_r4 Domain
IPR007624 RNA polymerase sigma-70 region 3 RNA_pol_sigma70_r3 Domain
IPR015189 Translation elongation factor SelB, winged helix, type 1 Elong_fac_SelB-wing-hlx_typ-1 Domain
IPR018335 Transcription regulator HTH, Crp-type, conserved site Tscrpt_reg_HTH_Crp-type_CS Conserved_site
IPR019885 Transcription regulator HTH, AsnC-type, conserved site Tscrpt_reg_HTH_AsnC-type_CS Conserved_site

67 Found In

Id Name Short Name Type
IPR000717 Proteasome component (PCI) domain PCI_dom Domain
IPR009374 Eukaryotic translation initiation factor 3 subunit K eIF3k Family
IPR003196 Transcription initiation factor IIF, beta subunit TFIIF_beta Family
IPR002717 MOZ/SAS-like protein MOZ_SAS Domain
IPR014892 Replication protein A, C-terminal RPA_C Domain
IPR008851 Transcription initiation factor IIF, alpha subunit TFIIF-alpha Family
IPR005819 Histone H5 Histone_H5 Family
IPR008339 Dishevelled family Dishevelled_fam Family
IPR002853 Transcription factor TFIIE, alpha subunit TFIIE_asu Family
IPR010906 Bacteriophage lambda, Nu1, terminase small subunit Phage_lambda_Nu1_terminase-ssu Family
IPR008341 Dishevelled-2 DVL2 Family
IPR014284 RNA polymerase sigma-70 like domain RNA_pol_sigma-70_dom Domain
IPR000943 RNA polymerase sigma-70 RNA_pol_sigma70 Domain
IPR012759 RNA polymerase sigma factor RpoH, proteobacteria RNA_pol_sigma_RpoH_proteobac Family
IPR019888 Transcription regulator AsnC-type Tscrpt_reg_AsnC-typ Family
IPR001367 Iron dependent repressor-like, metal binding and dimerisation domain Fe_dep_repressor Domain
IPR005650 BlaI transcriptional regulatory family BlaI_family Family
IPR004085 DNA topoisomerase VI, subunit A TopoVI_A Family
IPR019941 Transcription regulator LuxR, chaperone HchA-associated Tscrpt_reg_LuxR_HchA-assoc Family
IPR014646 Replication factor A protein 2 Rfa2/RPA32 Family
IPR016371 RNA polymerase sigma-H factor RNA_pol_sigma-H_factor Family
IPR014218 RNA polymerase sigma-H type RNA_pol_sigma-H Family
IPR016263 RNA polymerase sporulation-specific sigma factor, SigK/SigE RNA_pol_sigma-SigE/K Family
IPR014200 RNA polymerase sigma-E type RNA_pol_sigma-E Family
IPR014209 RNA polymerase sigma-K type RNA_pol_sigma-K Family
IPR016262 RNA polymerase sigma factor, SigB/SigC/SigD, plastid RNA_pol_sigma_SigB/C/D_plastid Family
IPR016461 O-methyltransferase COMT-type O-MeTrfase_COMT Family
IPR012967 Plant methyltransferase dimerisation Plant_MeTrfase_dimerisation Domain
IPR016481 Transcription factor TFE, archaea TF_E_archaea Family
IPR016723 Transcription regulator, ArsR, predicted Tscrpt_reg_ArsR_prd Family

0 Parent Features

8 Publications

First Author Title Year Journal Volume Pages
Yamada K Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery. 2002 Mol Cell 10 671-81
Wah DA Structure of the multimodular endonuclease FokI bound to DNA. 1997 Nature 388 97-100
Wilson KP Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. 1992 Proc Natl Acad Sci U S A 89 9257-61
Gajiwala KS Winged helix proteins. 2000 Curr Opin Struct Biol 10 110-6
Lai E Hepatocyte nuclear factor 3/fork head or "winged helix" proteins: a family of transcription factors of diverse biologic function. 1993 Proc Natl Acad Sci U S A 90 10421-3
Cicero MP The wing in yeast heat shock transcription factor (HSF) DNA-binding domain is required for full activity. 2001 Nucleic Acids Res 29 1715-23
Liu J Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. 2000 Mol Cell 6 637-48
Clubb RT The wing of the enhancer-binding domain of Mu phage transposase is flexible and is essential for efficient transposition. 1996 Proc Natl Acad Sci U S A 93 1146-50

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)