2QQ9

Crystal Structure of DtxR(D6A C102D) Complexed with Nickel(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Role of the N-Terminal Helix in the Metal Ion-Induced Activation of the Diphtheria Toxin Repressor DtxR.

D'Aquino, J.A.Lattimer, J.R.Denninger, A.D'Aquino, K.E.Ringe, D.

(2007) Biochemistry 46: 11761-11770

  • DOI: 10.1021/bi7007883
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The metal ion-regulated transcriptional repressor DtxR has been shown to repress the transcription of the diphtheria toxin and other genes associated with ferrous ion homeostasis in Corynebacterium diphtheriae. In vivo studies of single-alanine mutat ...

    The metal ion-regulated transcriptional repressor DtxR has been shown to repress the transcription of the diphtheria toxin and other genes associated with ferrous ion homeostasis in Corynebacterium diphtheriae. In vivo studies of single-alanine mutations located in the N-terminal helix of DtxR show that the activity of the mutants is reduced compared to that of the wild type. The three-dimensional structures of the apo and activated forms of DtxR show conformational changes in the N-terminal helix resulting from metal ion activation. We have studied the N-terminal helix mutants DtxR(D6A,C102D), DtxR(E9A,C102D), and DtxR(M10A,C102D) using crystallographic and calorimetric techniques to gain insight into the possible reasons for such behavior at a molecular level. The binding affinities for metal ion extracted from the calorimetric titrations of the mutants DtxR(D6A,C102D) and DtxR(E9A,C102D) are very similar to those found for DtxR(C102D), while the same experiments performed with the mutant DtxR(M10A,C102D), bearing the M10A mutation located in binding site 2, show a decreased binding affinity in a predictable fashion. These results suggest that the decreased activity observed in these mutants cannot be explained exclusively by changes in the binding affinity of the repressor. The crystal structures of Ni-DtxR(M10A,C102D), Ni-DtxR(E9A,C102D), and Ni-DtxR(D6A,C102D) clearly show the presence of two metal ions bound. In the structure of Ni-DtxR(M10A,C102D), a water replaces Met10 in binding site 2. In the structure of Ni-DtxR(D6A,C102D), the nonhelical conformation of the N-terminal region characteristic of the activated form is absent. The side chain of Asp6 is critical in stabilization of the nonhelical conformation. This conformation is identical in all high-resolution structures of activated DtxR with an intact N-terminal helix, suggesting relevance in DtxR's regulatory function.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diphtheria toxin repressor
A
226Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)Mutation(s): 2 
Gene Names: dtxR
Find proteins for P0DJL7 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Go to UniProtKB:  P0DJL7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.236 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 62.711α = 90.00
b = 62.711β = 90.00
c = 107.414γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata collection
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2018-04-04
    Type: Data collection