6Y42

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1021/jacs.9b12250
  • Primary Citation of Related Structures:  
    6Y42, 6Y45

  • PubMed Abstract: 

    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 p K a 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.


  • Organizational Affiliation

    Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rrf2 family transcriptional regulator
A, B
166Streptomyces venezuelae ATCC 10712Mutation(s): 0 
Gene Names: SVEN_6563
UniProt
Find proteins for F2RGC9 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745))
Explore F2RGC9 
Go to UniProtKB:  F2RGC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2RGC9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (39-MER)C [auth E]39Streptomyces venezuelae ATCC 10712
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (39-MER)D [auth F]39Streptomyces venezuelae ATCC 10712
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.268 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.37α = 90
b = 197.37β = 90
c = 73.19γ = 120
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
French National Research AgencyFranceANR-18-CE11-0010
French National Research AgencyFranceANR-10-INSB-05-02

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description