InterPro : IPR000445

Name  Helix-hairpin-helix motif Short Name  HhH_motif
Type  Conserved_site 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

6 Found In

Id Name Short Name Type
IPR011257 DNA glycosylase DNA_glycosylase Domain
IPR003265 HhH-GPD domain HhH-GPD_domain Domain
IPR004509 Competence protein ComEA, helix-hairpin-helix domain Competence_ComEA_HhH Domain
IPR005759 Endonuclease III Nth Family
IPR005760 A/G-specific adenine glycosylase MutY A/G_AdeGlyc_MutY Family
IPR004787 Competence protein ComEA Competence_ComE 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)