The helix-hairpin-helix DNA-binding motif: A structural basis for non-sequence-specific recognition of DNA

Doherty, Aidan J, Serpell, Louise C and Ponting, Christopher P (1996) The helix-hairpin-helix DNA-binding motif: A structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Research, 24 (13). pp. 2488-2497. ISSN 03051048

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Abstract

One, two or four copies of the 'helix-hairpin-helix' (HhH) DNA-binding motif are predicted to occur in 14 homologous families of proteins. The predicted DNA-binding function of this motif is shown to be consistent with the crystallographic structure of rat polymerase ß, complexed with DNA template-primer and with biochemical data. Five crystal structures of predicted HhH motifs are currently known: two from rat pol ß and one each in endonuclease III, AlkA and the 5' nuclease domain of Taq pol I. These motifs are more structurally similar to each other than to any other structure in current databases, including helix-turn-helix motifs. The clustering of the five HhH structures separately from other bi-helical structures in searches indicates that all members of the 14 families of proteins described herein possess similar HhH structures. By analogy with the rat pol ß structure, it is suggested that each of these HhH motifs bind DNA in a non-sequence-specific manner, via the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups. This type of interaction contrasts with the sequence-specific interactions of other motifs, including helix-turn-helix structures. Additional evidence is provided that alphaherpesvirus virion host shutoff proteins are members of the polymerase I 5'-nuclease and FEN1-like endonuclease gene family, and that a novel HhH-containing DNA-binding domain occurs in the kinesin-like molecule nod, and in other proteins such as cnjB, emb-5 and SPT6.

Item Type: Article
Schools and Departments: School of Life Sciences > Biochemistry
Depositing User: Louise Serpell
Date Deposited: 06 Feb 2012 20:12
Last Modified: 07 Mar 2017 15:11
URI: http://sro.sussex.ac.uk/id/eprint/24655

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