Conserved Site

Helix-turn-helix motif (IPR000047)

Short name: HTH_motif


Helix-turn-helix (HTH) motifs are found in all known DNA binding proteins that regulate gene expression. The motif consists of approximately 20 residues and is characterised by 2 alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix of the HTH motif 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 [PMID: 2644244]. The first helix helps to stabilise the structure [PMID: 6896364].

The HTH motif is very similar in sequence and structure to the N-terminal region of the lambda [PMID: 6236744] and other repressor proteins, and has also been identified in many other DNA-binding proteins on the basis of sequence and structural similarity [PMID: 2644244]. One of the principal differences between HTH motifs in these different proteins arises from the stereochemical requirement for glycine in the turn, which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and other repressors the Gly appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0003677 DNA binding

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.