Solution structure of the LexA repressor DNA binding domain determined by 1H NMR spectroscopy

Abstract

The structure of the 84 residue DNA binding domain of the Escherichia coli LexA repressor has been determined from NMR data using distance geometry and restrained molecular dynamics. The assignment of the 1(H) NMR spectrum of the molecule, derived from 2- and 3-D homonuclear experiments, is also reported. A total of 613 non-redundant distance restraints were used to give a final family of 28 structures. The structured region of the molecule consisted of residues 4-69 and yielded a r.m.s. deviation from an average of 0.9 Å for backbone and 1.6 Å for all heavy atoms. The structure contains three regular α-helices at residues 6-21(I), 28-35 (II) and 41-52 (III), and an antiparallel β-sheet at residues 56-58 and 66-68. Helices II and III form a variant helix-turn-helix DNA binding motif, with an unusual one residue insert at residue 38. The topology of the LexA DNA binding domain is found to be the same as for the DNA binding domains of the catabolic activator protein, human histone 5, the HNF-3/fork head protein and the Kluyveromyces lactis heat shock transcription factor.