1BI2

STRUCTURE OF APO-AND HOLO-DIPHTHERIA TOXIN REPRESSOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.257 

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

  • Primary Citation of Related Structures:  1BI0, 1BI1, 1BI3

  • 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: 
    • Purification and Characterization of the Diphtheria Toxin Repressor
      Schmitt, M.P.,Twiddy, E.M.,Holmes, R.K.
      (1992) Proc.Natl.Acad.Sci.USA 89: 7576
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIPHTHERIA TOXIN REPRESSOR
A, B
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.257 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.000α = 90.00
b = 63.000β = 90.00
c = 216.200γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance