1U8R

Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions.

Wisedchaisri, G.Holmes, R.K.Hol, W.G.J.

(2004) J.Mol.Biol. 342: 1155-1169

  • DOI: 10.1016/j.jmb.2004.07.083

  • PubMed Abstract: 
  • The iron-dependent regulator (IdeR) is an essential protein in Mycobacterium tuberculosis that regulates iron uptake in this major pathogen. Under high iron concentrations, IdeR binds to several operator regions and represses transcription of target ...

    The iron-dependent regulator (IdeR) is an essential protein in Mycobacterium tuberculosis that regulates iron uptake in this major pathogen. Under high iron concentrations, IdeR binds to several operator regions and represses transcription of target genes. Here, we report the first crystal structure of cobalt-activated IdeR bound to the mbtA-mbtB operator at 2.75 A resolution. IdeR binds to the DNA as a "double-dimer" complex with two dimers on opposite sides of the DNA duplex with the dimer axes deviating approximately 157 degrees. The asymmetric unit contains two such double-dimer complexes with a total molecular mass of 240 kDa. Two metal-binding sites are fully occupied with the SH3-like third domain adopting a "wedge" position to interact with the two other domains, and providing two ligands for the metal site 1 in all eight subunits per asymmetric unit. A putative sodium ion is observed to mediate interactions between Asp35 and DNA. There is a conformational change in the DNA-binding domain caused by a 6-9 degrees rotation of the helix-turn-helix motif with respect to the rest of the molecule upon binding to the DNA. Ser37 and Pro39 make specific interactions with conserved thymine bases while Gln43 makes non-specific contacts with different types of bases in different subunits. A "p1s2C3T4a5" base recognition pattern is proposed to be the basis for key interactions for each IdeR subunit with the DNA in the IdeR-DNA complex structure.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Iron-dependent repressor ideR
A, B, C, D, G, H, I, J
230Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ideR (dtxR)
Find proteins for P9WMH1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WMH1
Entity ID: 1
MoleculeChainsLengthOrganism
mbtA operator DNAE,K33N/A
Entity ID: 2
MoleculeChainsLengthOrganism
mbtB operator DNAF,L33N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, G, H, I, J
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, B, C, D, G, H, I, J
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.230 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 107.959α = 90.00
b = 107.959β = 90.00
c = 215.124γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance