The solution structures of the trp repressor-operator DNA complex

Hong Zhang, Daqing Zhao, Matthew Revington, Weon Tae Lee, Xin Jia, Cheryl Arrowsmith, Oleg Jardetzky

Research output: Contribution to journalArticle

105 Citations (Scopus)

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) Å for the repressor backbone, 1·1(± 0·5) Å for the DNA backbone, and 1·3(± 0·3) Å 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(η1) and NH(η2) 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.

Original languageEnglish
Pages (from-to)592-614
Number of pages23
JournalJournal of Molecular Biology
Volume238
Issue number4
DOIs
Publication statusPublished - 1994 May 12

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DNA
Base Pairing
E coli TRPR protein
Molecular Dynamics Simulation
Tryptophan
Protons
Hydrogen
Escherichia coli

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

Zhang, H., Zhao, D., Revington, M., Lee, W. T., Jia, X., Arrowsmith, C., & Jardetzky, O. (1994). The solution structures of the trp repressor-operator DNA complex. Journal of Molecular Biology, 238(4), 592-614. https://doi.org/10.1006/jmbi.1994.1317
Zhang, Hong ; Zhao, Daqing ; Revington, Matthew ; Lee, Weon Tae ; Jia, Xin ; Arrowsmith, Cheryl ; Jardetzky, Oleg. / The solution structures of the trp repressor-operator DNA complex. In: Journal of Molecular Biology. 1994 ; Vol. 238, No. 4. pp. 592-614.
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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) {\AA} for the repressor backbone, 1·1(± 0·5) {\AA} for the DNA backbone, and 1·3(± 0·3) {\AA} 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(η1) and NH(η2) 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.",
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Zhang, H, Zhao, D, Revington, M, Lee, WT, Jia, X, Arrowsmith, C & Jardetzky, O 1994, 'The solution structures of the trp repressor-operator DNA complex', Journal of Molecular Biology, vol. 238, no. 4, pp. 592-614. https://doi.org/10.1006/jmbi.1994.1317

The solution structures of the trp repressor-operator DNA complex. / Zhang, Hong; Zhao, Daqing; Revington, Matthew; Lee, Weon Tae; Jia, Xin; Arrowsmith, Cheryl; Jardetzky, Oleg.

In: Journal of Molecular Biology, Vol. 238, No. 4, 12.05.1994, p. 592-614.

Research output: Contribution to journalArticle

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T1 - The solution structures of the trp repressor-operator DNA complex

AU - Zhang, Hong

AU - Zhao, Daqing

AU - Revington, Matthew

AU - Lee, Weon Tae

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N2 - 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) Å for the repressor backbone, 1·1(± 0·5) Å for the DNA backbone, and 1·3(± 0·3) Å 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(η1) and NH(η2) 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.

AB - 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) Å for the repressor backbone, 1·1(± 0·5) Å for the DNA backbone, and 1·3(± 0·3) Å 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(η1) and NH(η2) 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.

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