1DDN

DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex.

White, A.Ding, X.vanderSpek, J.C.Murphy, J.R.Ringe, D.

(1998) Nature 394: 502-506

  • DOI: 10.1038/28893
  • Primary Citation of Related Structures:  2TDX
  • Also Cited By: 2H09

  • PubMed Abstract: 
  • The virulent phenotype of the pathogenic bacterium Corynebacterium diphtheriae is conferred by diphtheria toxin, whose expression is an adaptive response to low concentrations of iron. The expression of the toxin gene (tox) is regulated by the repres ...

    The virulent phenotype of the pathogenic bacterium Corynebacterium diphtheriae is conferred by diphtheria toxin, whose expression is an adaptive response to low concentrations of iron. The expression of the toxin gene (tox) is regulated by the repressor DtxR, which is activated by transition metal ions. X-ray crystal structures of DtxR with and without (apo-form) its coordinated transition metal ion have established the general architecture of the repressor, identified the location of the metal-binding sites, and revealed a metal-ion-triggered subunit-subunit 'caliper-like' conformational change. Here we report the three-dimensional crystal structure of the complex between a biologically active Ni(II)-bound DtxR(C102D) mutant, in which a cysteine is replaced by an aspartate at residue 102, and a 33-base-pair DNA segment containing the toxin operator toxO. This structure shows that DNA interacts with two dimeric repressor proteins bound to opposite sides of the tox operator. We propose that a metal-ion-induced helix-to-coil structural transition in the amino-terminal region of the protein is partly responsible for the unique mode of repressor activation by transition metal ions.


    Related Citations: 
    • Identification of the Primary Metal Ion-Activation Sites of the Diphtheria Tox Repressor by X-Ray Crystallography and Site-Directed Mutational Analysis
      Ding, X.,Zeng, H.,Schiering, N.,Ringe, D.,Murphy, J.R.
      (1996) Nat.Struct.Mol.Biol. 3: 382
    • Cysteine-102 is Positioned in the Metal Binding Activation Site of the Corynebacterium Diphtheriae Regulatory Element Dtxr
      Tao, X.,Murphy, J.R.
      (1993) Proc.Natl.Acad.Sci.USA 90: 8524
    • Structures of the Apo-and the Metal Ion-Activated Forms of the Diphtheria Tox Repressor from Corynebacterium Diphtheriae
      Schiering, N.,Tao, X.,Zeng, H.,Murphy, J.R.,Petsko, G.A.,Ringe, D.
      (1995) Proc.Natl.Acad.Sci.USA 92: 9843


    Organizational Affiliation

    Rosenstiel Basic Medical Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DIPHTHERIA TOX REPRESSOR
A, B, C, D
226Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)Gene Names: dtxR
Find proteins for P0DJL7 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Go to UniProtKB:  P0DJL7
Entity ID: 1
MoleculeChainsLengthOrganism
33 BASE DNA CONTAINING TOXIN OPERATORE33N/A
Entity ID: 2
MoleculeChainsLengthOrganism
33 BASE DNA CONTAINING TOXIN OPERATORF33N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A, B, C, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 117.050α = 90.00
b = 117.050β = 90.00
c = 145.340γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance