6Y42

Crystal Structure of RsrR complexed to a 39 basepair DNA fragment of the rsrR promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Electron and Proton Transfers Modulate DNA Binding by the Transcription Regulator RsrR.

Crack, J.C.Amara, P.Volbeda, A.Mouesca, J.M.Rohac, R.Pellicer Martinez, M.T.Huang, C.Y.Gigarel, O.Rinaldi, C.Le Brun, N.E.Fontecilla-Camps, J.C.

(2020) J.Am.Chem.Soc. 142: 5104-5116

  • DOI: 10.1021/jacs.9b12250
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The [Fe <sub>2 </sub>S <sub>2 </sub>]-RsrR gene transcription regulator senses the redox status in bacteria by modulating DNA binding while its cluster cycles between +1 and +2 states - only the latter binds DNA. We have previously shown that RsrR ca ...

    The [Fe 2 S 2 ]-RsrR gene transcription regulator senses the redox status in bacteria by modulating DNA binding while its cluster cycles between +1 and +2 states - only the latter binds DNA. We have previously shown that RsrR can undergo remarkable conformational changes involving a 100° rotation of tryptophan 9 between exposed ( Out ) and buried ( In ) states. Here, we have used the chemical modification of Trp9, site-directed mutagenesis and crystallographic and computational chemical studies to show that (i) the Out and In states correspond to oxidized and reduced RsrR, respectively, (ii) His33 is protonated in the In state due to a change in its pKa caused by cluster reduction and (iii) Trp9 rotation is conditioned by the response of its dipole moment to environmental electrostatic changes. Our findings illustrate a novel function of protonation resulting from electron transfer.


    Related Citations: 
    • Crystal Structure of the Transcription Regulator RsrR Reveals a [2Fe-2S] Cluster Coordinated by Cys, Glu, and His Residues.
      Volbeda, A.,Martinez, M.T.P.,Crack, J.C.,Amara, P.,Gigarel, O.,Munnoch, J.T.,Hutchings, M.I.,Darnault, C.,Le Brun, N.E.,Fontecilla-Camps, J.C.
      (2019) J. Am. Chem. Soc. 141: 2367



Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rrf2 family transcriptional regulator
A, B
166Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745)Mutation(s): 0 
Find proteins for F2RGC9 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745))
Go to UniProtKB:  F2RGC9
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (39-MER)E39Streptomyces venezuelae ATCC 10712
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (39-MER)F39Streptomyces venezuelae ATCC 10712
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.267 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 197.370α = 90.00
b = 197.370β = 90.00
c = 73.190γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-18-CE11-0010
French National Research AgencyFranceANR-10-INSB-05-02

Revision History 

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-25
    Type: Database references