1DDN image
Deposition Date 1998-06-23
Release Date 1998-10-14
Last Version Date 2023-08-02
Entry Detail
PDB ID:
1DDN
Title:
DIPHTHERIA TOX REPRESSOR (C102D MUTANT)/TOX DNA OPERATOR COMPLEX
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.28
R-Value Work:
0.24
Space Group:
P 41
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DIPHTHERIA TOX REPRESSOR
Mutations:C102D
Chain IDs:C (auth: A), D (auth: B), E (auth: C), F (auth: D)
Chain Length:226
Number of Molecules:4
Biological Source:Corynebacterium diphtheriae
Ligand Molecules
Primary Citation
Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex.
Nature 394 502 506 (1998)
PMID: 9697776 DOI: 10.1038/28893

Abstact

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.

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Primary Citation of related structures