1BI3

STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR.

Pohl, E.Holmes, R.K.Hol, W.G.

(1998) J Biol Chem 273: 22420-22427

  • DOI: 10.1074/jbc.273.35.22420
  • Primary Citation of Related Structures:  
    1BI3, 1BI2, 1BI1, 1BI0

  • PubMed Abstract: 
  • The diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae is a divalent metal-activated repressor of chromosomal genes that encode proteins responsible for siderophore-mediated iron uptake and also of the gene of certain corynebacterioph ...

    The diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae is a divalent metal-activated repressor of chromosomal genes that encode proteins responsible for siderophore-mediated iron uptake and also of the gene of certain corynebacteriophages that encodes diphtheria toxin. DtxR consists of two 25.3-kDa three-domain subunits and is a member of a family of related repressor proteins in several Gram-positive bacterial species, some of which are important human pathogens. In this paper, we report on the first high resolution crystal structures of apo-DtxR in two related space groups. In addition, crystal structures of Zn-DtxR were determined in the same two space groups. The resolutions of the structures range from 2.2 to 2.4 A. The four refined models of the apo- and the holo-repressor exhibit quite similar metal binding centers, which do, however, show higher thermal motion in the apo-structures. All four structures reported differ from each other in one important aspect. The N-terminal DNA-binding domain and the last 20 residues of the dimerization domain of each subunit move significantly with respect to the core of the DtxR dimer, which consists of residues 74-120 from both subunits. These results provide the first indication of a conformational change that may occur upon binding of the holo-repressor to DNA.


    Related Citations: 
    • Three-Dimensional Structure of the Diphtheria Toxin Repressor in Complex with Divalent Cation Co-Repressors
      Qiu, X., Verlinde, C.L., Zhang, S., Schmitt, M.P., Holmes, R.K., Hol, W.G.
      (1995) Structure 3: 87
    • Purification and Characterization of the Diphtheria Toxin Repressor
      Schmitt, M.P., Twiddy, E.M., Holmes, R.K.
      (1992) Proc Natl Acad Sci U S A 89: 7576

    Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle, Washington 98195-7742, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIPHTHERIA TOXIN REPRESSORA, B226Corynebacterium diphtheriaeMutation(s): 1 
Gene Names: dtxR
Find proteins for P0DJL7 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore P0DJL7 
Go to UniProtKB:  P0DJL7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
A,BL-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.4α = 90
b = 63.4β = 90
c = 213.2γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1998-06-21 
  • Released Date: 1999-06-22 
  • Deposition Author(s): Pohl, E., Hol, W.G.J.

Revision History 

  • Version 1.0: 1999-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance