7B24

DtxR-like iron-dependent regulator IdeR (P39G variant) complexed with cobalt and its consensus DNA-binding sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.3 of the entry. See complete history


Literature

The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout.

Marcos-Torres, F.J.Maurer, D.Juniar, L.Griese, J.J.

(2021) Nucleic Acids Res 49: 10120-10135

  • DOI: https://doi.org/10.1093/nar/gkab711
  • Primary Citation of Related Structures:  
    7B1V, 7B1Y, 7B20, 7B23, 7B24, 7B25

  • PubMed Abstract: 

    The iron-dependent regulator IdeR is the main transcriptional regulator controlling iron homeostasis genes in Actinobacteria, including species from the Corynebacterium, Mycobacterium and Streptomyces genera, as well as the erythromycin-producing bacterium Saccharopolyspora erythraea. Despite being a well-studied transcription factor since the identification of the Diphtheria toxin repressor DtxR three decades ago, the details of how IdeR proteins recognize their highly conserved 19-bp DNA target remain to be elucidated. IdeR makes few direct contacts with DNA bases in its target sequence, and we show here that these contacts are not required for target recognition. The results of our structural and mutational studies support a model wherein IdeR mainly uses an indirect readout mechanism, identifying its targets via the sequence-dependent DNA backbone structure rather than through specific contacts with the DNA bases. Furthermore, we show that IdeR efficiently recognizes a shorter palindromic sequence corresponding to a half binding site as compared to the full 19-bp target previously reported, expanding the number of potential target genes controlled by IdeR proteins.


  • Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DtxR family iron (Metal) dependent repressor233Saccharopolyspora erythraea NRRL 2338Mutation(s): 1 
Gene Names: A8924_2181
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
consensus DNA-binding sequence30synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
consensus DNA-binding sequence30synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.395α = 90
b = 113.841β = 117.25
c = 89.795γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03770

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 2.0: 2021-03-31
    Type: Coordinate replacement
    Reason: Polymer geometry
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 3.0: 2021-07-28
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 3.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 3.2: 2021-10-06
    Changes: Data collection, Database references
  • Version 3.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description