The solution structures of the trp repressor-operator DNA complex.Zhang, H., Zhao, D., Revington, M., Lee, W., Jia, X., Arrowsmith, C., Jardetzky, O.
(1994) J.Mol.Biol. 238: 592-614
- PubMed: 8176748
- DOI: 10.1006/jmbi.1994.1317
- PubMed Abstract:
- Refined Solution Structures of the Escherichia Coli Trp Holo-and Aporepressor
Zhao, D.,Arrowsmith, C.H.,Jia, X.,Jardetzky, O.
(1993) J.Mol.Biol. 229: 735
- Sequential Simulated Annealing: An Efficient Procedure for Structural Refinement Based on NMR Constraints
Zhao, D.,Jardetzky, O.
(1993) J.Phys.Chem. 97: 3007
- Sequence-Specific 1H NMR Assignments and Secondary Structure in Solution of Escherichia Coli Trp Repressor
Arrowsmith, C.H.,Pachter, R.,Altman, R.B.,Iyer, S.B.,Jardetzky, O.
(1990) Biochemistry 29: 6332
- The Solution Structures of Escherichia Coli Trp Repressor and Trp Aporepressor at an Intermediate Resolution
Arrowsmith, C.,Pachter, R.,Altman, R.,Jardetzky, O.
(1991) Eur.J.Biochem. 202: 53
- NMR Assignments for the Amino-Terminal Residues of Trp Repressor and Their Role in DNA Binding
Arrowsmith, C.H.,Carey, J.,Treat-Clemons, L.,Jardetzky, O.
(1989) Biochemistry 28: 3875
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 homonucle ...
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.
Stanford Magnetic Resonance Laboratory, CA 94305-5055.