A modelled tertiary structure for the dimeric HLH domain of the E47 protein is presented. Structural information was obtained from the aligned sequences of > 40 members of the HLH family. The information was used to model each monomer as an alpha-helical hairpin, with knobs-into-holes packing of side-chains as found in antiparallel coiled-coil. The dimer forms a four-helix bundle with additional knobs-into-holes packing at the dimer interface. The size and electrostatic properties of core-forming residues are all accounted for in the model. The model does not violate any known properties of protein structure. The monomers are related by two-fold rotational symmetry, in agreement with the observed DNA-binding sites which are imperfect inverted repeats. The N-terminal basic region, in which DNA binding and base specificity reside, forms the first part of helix 1. A prediction based on the model structure is that the HLH domains do not bind to DNA in its B form but require a partially unwound conformation in order to enter the major groove.
Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins.,Gibson TJ, Thompson JD, Abagyan RA Protein Eng. 1993 Jan;6(1):41-50. PMID:8433970[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
↑ Gibson TJ, Thompson JD, Abagyan RA. Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins. Protein Eng. 1993 Jan;6(1):41-50. PMID:8433970
