1RCS

NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • DOI: 10.1006/jmbi.1994.1317

  • 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 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.


    Related Citations: 
    • 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


    Organizational Affiliation

    Stanford Magnetic Resonance Laboratory, CA 94305-5055.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRP REPRESSOR
A, B
105Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: trpR (rtrY)
Find proteins for P0A881 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A881
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*AP*CP*G)-3')E,F20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download SDF File 
Download CCD File 
A, B
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 
  • Olderado: 1RCS Olderado
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-05-12 
  • Released Date: 1996-06-20 
  • Deposition Author(s): Zhao, D., Zheng, Z.

Revision History 

  • Version 1.0: 1996-06-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance