1DDN

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

• PDB DOI:  https://doi.org/10.2210/pdb1DDN/pdb
• NAKB: 1DDN

• Classification: GENE REGULATION/DNA
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-06-23 Released: 1998-10-14 
• Deposition Author(s): White, A., Ding, X., Vanderspek, J.C., Murphy, J.R., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.240 

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

• PubMed: 9697776 
• 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.

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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 Biol 3: 382

• 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 U S A 92: 9843

• 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 U S A 90: 8524

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 122.21 kDa 
• Atom Count: 5,135 
• Modelled Residue Count: 538 
• Deposited Residue Count: 970 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPHTHERIA TOX REPRESSOR	C [auth A], D [auth B], E [auth C], F [auth D]	226	Corynebacterium diphtheriae	Mutation(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 ID: 1
Molecule	Chains	Length	Organism	Image
33 BASE DNA CONTAINING TOXIN OPERATOR	A [auth E]	33	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
33 BASE DNA CONTAINING TOXIN OPERATOR	B [auth F]	33	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.240 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.05	α = 90
b = 117.05	β = 90
c = 145.34	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): White, A., Ding, X., Vanderspek, J.C., Murphy, J.R., Ringe, D.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-02
  Changes: Refinement description