1B1B

IRON DEPENDENT REGULATOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the iron-dependent regulator (IdeR) from Mycobacterium tuberculosis shows both metal binding sites fully occupied.

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

(1999) J Mol Biol 285: 1145-1156

  • DOI: 10.1006/jmbi.1998.2339
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Iron-dependent regulators are a family of metal-activated DNA binding proteins found in several Gram-positive bacteria. These proteins are negative regulators of virulence factors and of proteins of bacterial iron-uptake systems. In this study we pre ...

    Iron-dependent regulators are a family of metal-activated DNA binding proteins found in several Gram-positive bacteria. These proteins are negative regulators of virulence factors and of proteins of bacterial iron-uptake systems. In this study we present the crystal structure of the iron-dependent regulator (IdeR) from Mycobacterium tuberculosis, the causative agent of tuberculosis. The protein crystallizes in the hexagonal space group P62 with unit cell dimensions a=b=92.6 A, c=63.2 A. The current model comprises the N-terminal DNA-binding domain (residues 1-73) and the dimerization domain (residues 74-140), while the third domain (residues 141-230) is too disordered to be included. The molecule lies on a crystallographic 2-fold axis that generates the functional dimer. The overall structure of the monomer shares many features with the homologous regulator, diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae. The IdeR structure in complex with Zinc reported here is, however, the first wild-type repressor structure with both metal binding sites fully occupied. This crystal structure reveals that both Met10 and most probably the Sgamma of Cys102 are ligands of the second metal binding site. In addition, there are important changes in the tertiary structure between apo-DtxR and holo-IdeR bringing the putative DNA binding helices closer together in the holo repressor. The mechanism by which metal binding may cause these structural changes between apo and holo wild-type repressor is discussed.


    Organizational Affiliation

    Departments of Biological Structure and Biochemistry, Biomolecular Structure Center.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (IRON DEPENDENT REGULATOR)
A
140Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WMH1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WMH1
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.360 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.6α = 90
b = 92.6β = 90
c = 63.2γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-03
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance