4HF0 | pdb_00004hf0

Crystal Structure of Apo IscR

• PDB DOI: https://doi.org/10.2210/pdb4HF0/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-04 Released: 2013-05-08 
• Deposition Author(s): Rajagopalan, S.R., Phillips, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.221 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity.

Rajagopalan, S., Teter, S.J., Zwart, P.H., Brennan, R.G., Phillips, K.J., Kiley, P.J.

(2013) Nat Struct Mol Biol 20: 740-747

• PubMed: 23644595 
• DOI: https://doi.org/10.1038/nsmb.2568
• Primary Citation Related Structures: 
  4HF0, 4HF1, 4HF2


• PubMed Abstract: 
  

  IscR from Escherichia coli is an unusual metalloregulator in that both apo and iron sulfur (Fe-S)-IscR regulate transcription and exhibit different DNA binding specificities. Here, we report structural and biochemical studies of IscR suggesting that remodeling of the protein-DNA interface upon Fe-S ligation broadens the DNA binding specificity of IscR from binding the type 2 motif only to both type 1 and type 2 motifs. Analysis of an apo-IscR variant with relaxed target-site discrimination identified a key residue in wild-type apo-IscR that, we propose, makes unfavorable interactions with a type 1 motif. Upon Fe-S binding, these interactions are apparently removed, thereby allowing holo-IscR to bind both type 1 and type 2 motifs. These data suggest a unique mechanism of ligand-mediated DNA site recognition, whereby metallocluster ligation relocates a protein-specificity determinant to expand DNA target-site selection, allowing a broader transcriptomic response by holo-IscR.

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Organizational Affiliation: 
• Genomic Medicine Program, The Methodist Hospital Research Institute, Houston, Texas, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.96 kDa 
• Atom Count: 1,785 
• Modeled Residue Count: 238 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator IscR	A, B	141	Escherichia coli K-12	Mutation(s): 3  Gene Names: iscR, yfhP, b2531, JW2515
UniProt
Find proteins for P0AGK8 (Escherichia coli (strain K12)) Explore P0AGK8  Go to UniProtKB:  P0AGK8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.221 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.85	α = 90
b = 88.85	β = 90
c = 62.734	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Rajagopalan, S.R., Phillips, K.J.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Database references
• Version 1.2: 2013-07-03
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations