1RCS

NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX

Summary for 1RCS

• Entry DOI: 10.2210/pdb1rcs/pdb
• Descriptor: DNA (5'-D(*CP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*AP*CP*G)-3'), TRP REPRESSOR, TRYPTOPHAN (3 entities in total)
• Functional Keywords: transcription regulation, repressor, dna-binding, trp, dna, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A881
• Total number of polymer chains: 4
• Total formula weight: 36753.89

Authors

Zhao, D.,Zheng, Z. (deposition date: 1995-05-12, release date: 1996-06-20, Last modification date: 2024-05-22)

Primary citation

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

PubMed Abstract: 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.

PubMed: 8176748
DOI: 10.1006/jmbi.1994.1317

Experimental method

SOLUTION NMR