InterPro : IPR003583

Name  Helix-hairpin-helix DNA-binding motif, class 1 Short Name  Hlx-hairpin-Hlx_DNA-bd_motif
Type  Domain Description  The HhH motif is a stretch of approximately 20 amino acids that is present in prokaryotic andeukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of thesemotifs have two helices connected by a short turn. In the HtH motif the secondhelix binds to DNA with the helix in the major groove. This allows the contactbetween specific base and residues throughout the protein. In the HhH motifthe second helix does not protrude from the surface of the protein andtherefore cannot lie in the major groove of the DNA. Crystallographic studiessuggest that the interaction of the HhH domain with DNA is mediated by aminoacids located in the strongly conserved loop (L-P-G-V) and at the N-terminalend of the second helix []. This interaction could involve the formation ofhydrogen bonds between protein backbone nitrogens and DNA phosphate groups[]. The structural difference between the HtH and HhH domains is reflected at thefunctional level: whereas the HtH domain, found primarily in gene regulatoryproteins and binds DNA in a sequence specific manner, the HhH domain is ratherfound in proteins involved in enzymatic activities and binds DNA with nosequence specificity [].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



0 Child Features

0 Contains

24 Found In

Id Name Short Name Type
IPR011257 DNA glycosylase DNA_glycosylase Domain
IPR003265 HhH-GPD domain HhH-GPD_domain Domain
IPR010996 DNA polymerase beta-like, N-terminal domain DNA_pol_b-like_N Domain
IPR010994 RuvA domain 2-like RuvA_2-like Domain
IPR010995 DNA repair Rad51/transcription factor NusA, alpha-helical DNA_repair_Rad51/TF_NusA_a-hlx Domain
IPR018320 DNA polymerase 1 DNA_polymerase_1 Family
IPR011941 DNA recombination/repair protein Rad51 DNA_recomb/repair_Rad51 Family
IPR004509 Competence protein ComEA, helix-hairpin-helix domain Competence_ComEA_HhH Domain
IPR000085 Bacterial DNA recombination protein RuvA RuvA Family
IPR000093 DNA recombination protein RecR DNA_Rcmb_RecR Family
IPR005759 Endonuclease III Nth Family
IPR001679 NAD-dependent DNA ligase DNAligase Family
IPR002008 DNA polymerase family X, beta-like DNA_pol_X_beta-like Family
IPR022311 Uncharacterised conserved protein UCP005047, YshC UCP005047_YshC Family
IPR005760 A/G-specific adenine glycosylase MutY A/G_AdeGlyc_MutY Family
IPR002054 DNA-directed DNA polymerase X DNA-dir_DNA_pol_X Domain
IPR004787 Competence protein ComEA Competence_ComE Family
IPR016467 DNA recombination and repair protein, RecA-like DNA_recomb/repair_RecA-like Family
IPR011938 DNA recombination/repair protein RadA DNA_recomb/repair_RadA Family
IPR011940 Meiotic recombinase Dmc1 DMC1_rcmbase Family
IPR004791 UvrABC system, subunit C UvrC Family
IPR016960 Uncharacterised conserved protein UCP030823, kinase, HhH DNA-binding UCP030823_PK_HhH Family
IPR012401 DNA-binding protein MutS2, archaea DNA-bd_MutS2_arc Family
IPR006345 DNA helicase, RecD/TraA type DNA_helicase_RecD/TraA Family

0 Parent Features

4 Publications

First Author Title Year Journal Volume Pages
Doherty AJ The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. 1996 Nucleic Acids Res 24 2488-97
Aravind L Conserved domains in DNA repair proteins and evolution of repair systems. 1999 Nucleic Acids Res 27 1223-42
Thayer MM Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. 1995 EMBO J 14 4108-20
Provvedi R ComEA is a DNA receptor for transformation of competent Bacillus subtilis. 1999 Mol Microbiol 31 271-80

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)