2TDX

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1038/28893
  • Primary Citation of Related Structures:  
    1DDN, 2TDX

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIPHTHERIA TOX REPRESSOR226Corynebacterium diphtheriaeMutation(s): 1 
Gene Names: DTXR
UniProt
Find proteins for P0DJL7 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore P0DJL7 
Go to UniProtKB:  P0DJL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DJL7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.5α = 90
b = 64.5β = 90
c = 105.7γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
R-AXISdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-08-09
    Changes: Refinement description
  • Version 1.5: 2024-05-22
    Changes: Data collection