PDBsum entry 1hlh

DNA-binding regulatory protein

PDB id: 1hlh

Contents

Protein chains

64 a.a.

Theoretical model

PDB id:

1hlh

Name:

DNA-binding regulatory protein

Structure:

E47 protein product of the e2a gene (helix-loop-helix domain) (theoretical model)

Source:

Human (homo sapiens)

Authors:

T.J.Gibson,J.D.Thompson,R.A.Abagyan

Key ref:

T.J.Gibson et al. (1993). Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins. Protein Eng, 6, 41-50. PubMed id: 8433970

Date:

10-Dec-92 Release date: 31-Jan-94

Protein chains

No UniProt id for this chain

Struc: 64 a.a.

Protein Eng 6:41-50 (1993)

PubMed id: 8433970

Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins.

T.J.Gibson, J.D.Thompson, R.A.Abagyan.

ABSTRACT

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.