5N07

Structure of the [4Fe-4S] form of the NO response regulator NsrR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding.

Volbeda, A.Dodd, E.L.Darnault, C.Crack, J.C.Renoux, O.Hutchings, M.I.Le Brun, N.E.Fontecilla-Camps, J.C.

(2017) Nat Commun 8: 15052-15052

  • DOI: 10.1038/ncomms15052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NsrR from Streptomyces coelicolor (Sc) regulates the expression of three genes through the progressive degradation of its [4Fe-4S] cluster on nitric oxide (NO) exposure. We report the 1.95 Å resolution crystal structure of dimeric holo-ScNsrR and sho ...

    NsrR from Streptomyces coelicolor (Sc) regulates the expression of three genes through the progressive degradation of its [4Fe-4S] cluster on nitric oxide (NO) exposure. We report the 1.95 Å resolution crystal structure of dimeric holo-ScNsrR and show that the cluster is coordinated by the three invariant Cys residues from one monomer and, unexpectedly, Asp8 from the other. A cavity map suggests that NO displaces Asp8 as a cluster ligand and, while D8A and D8C variants remain NO sensitive, DNA binding is affected. A structural comparison of holo-ScNsrR with an apo-IscR-DNA complex shows that the [4Fe-4S] cluster stabilizes a turn between ScNsrR Cys93 and Cys99 properly oriented to interact with the DNA backbone. In addition, an apo ScNsrR structure suggests that Asn97 from this turn, along with Arg12, which forms a salt-bridge with Asp8, are instrumental in modulating the position of the DNA recognition helix region relative to its major groove.


    Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale, CEA, CNRS, Université Grenoble-Alpes, 71, avenue des Martyrs, CS 10090, 38044 Grenoble cedex 9, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional repressor NsrR
A
161Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)Mutation(s): 0 
Gene Names: nsrR
Find proteins for Q9L132 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  Q9L132
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.760α = 90.00
b = 78.760β = 90.00
c = 93.260γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references