1rcs

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NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX

Overview

The solution structures of the complex between Escherichia coli trp, holorepressor and a 20 base-pair consensus operator DNA were determined., The majority of proton chemical shifts of the trp holorepressor and, operator DNA were assigned from homonuclear 2D NOESY spectra of, selectively deuterated analog-operator DNA complexes and the 3D NOESY-HMQC, spectrum of a uniformly 15N-labeled repressor-operator DNA complex. The, structures were calculated using restrained molecular dynamics and, sequential simulated annealing with 4086 NOE and other experimental, constraints. The root-mean-squared deviation (RMSD) among the calculated, structures and their mean is 0.9(+/- 0.3)A for the repressor backbone, 1.1(+/- 0.5)A for the DNA backbone, and 1.3(+/- 0.3)A for all heavy atoms., The DNA is deformed to a significant extent from the standard B DNA, structure to fit the helix-turn-helix (HTH) segment of the repressor, (helices D and E) into its major grooves. Little change is found in the, ABCF core of the repressor on complexation in comparison to the free, repressor, but changes in the cofactor L-tryptophan binding pocket and the, HTH segment are observed. The N-terminal residues (2 to 17) are found to, be disordered and do not form stable interactions with DNA. Direct, H-bonding to the bases of the operator DNA is consistent with all of our, observed NOE constraints. Hydrogen bonds from NH eta 1 and NH eta 2 of, Arg69 to O-6 and N-7 of G2 are compatible with the solution structure, as, they are with the crystal structure. Other direct H-bonds from Lys72, Ala80, Ile79, Thr83 and Arg84 to base-pair functional groups can also be, formed in our solution structures.

About this Structure

1RCS is a Single protein structure of sequence from Escherichia coli with TRP as ligand. Full crystallographic information is available from OCA.

Reference

The solution structures of the trp repressor-operator DNA complex., Zhang H, Zhao D, Revington M, Lee W, Jia X, Arrowsmith C, Jardetzky O, J Mol Biol. 1994 May 13;238(4):592-614. PMID:8176748

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