4U0Y

Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR.

Fillenberg, S.B., Grau, F.C., Seidel, G., Muller, Y.A.

(2015) Nucleic Acids Res 43: 1283-1296

  • DOI: 10.1093/nar/gku1374
  • Primary Citation of Related Structures:  
    4U0W, 4U0Y, 4U0V, 4WWC

  • PubMed Abstract: 

    • The uptake and metabolism of N-acetylglucosamine (GlcNAc) in Bacillus subtilis is controlled by NagR (formerly named YvoA), a member of the widely-occurring GntR/HutC family of transcription regulators. Upon binding to specific DNA operator sites (dre-sites) NagR blocks the transcription of genes for GlcNAc utilization and interaction of NagR with effectors abrogates gene repression ...

    The uptake and metabolism of N-acetylglucosamine (GlcNAc) in Bacillus subtilis is controlled by NagR (formerly named YvoA), a member of the widely-occurring GntR/HutC family of transcription regulators. Upon binding to specific DNA operator sites (dre-sites) NagR blocks the transcription of genes for GlcNAc utilization and interaction of NagR with effectors abrogates gene repression. Here we report crystal structures of NagR in complex with operator DNA and in complex with the putative effector molecules glucosamine-6-phosphate (GlcN-6-P) and N-acetylglucosamine-6-phosphate (GlcNAc-6-P). A comparison of the distinct conformational states suggests that effectors are able to displace the NagR-DNA-binding domains (NagR-DBDs) by almost 70 Å upon binding. In addition, a high-resolution crystal structure of isolated NagR-DBDs in complex with palindromic double-stranded DNA (dsDNA) discloses both the determinants for highly sequence-specific operator dre-site recognition and for the unspecific binding of NagR to dsDNA. Extensive biochemical binding studies investigating the affinities of full-length NagR and isolated NagR-DBDs for either random DNA, dre-site-derived palindromic or naturally occurring non-palindromic dre-site sequences suggest that proper NagR function relies on an effector-induced fine-tuning of the DNA-binding affinities of NagR and not on a complete abrogation of its DNA binding.

    Organizational Affiliation: 

    Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestrasse 91, D-91052 Erlangen, Germany yves.muller@fau.de.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HTH-type transcriptional repressor YvoA A, B, C, D78Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yvoA, BSU35030, nagR
Find proteins for O34817 (Bacillus subtilis (strain 168))
Explore O34817 
Go to UniProtKB:  O34817
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-3')E, F15Bacillus subtilis subsp. subtilis str. 168
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CL
    Query on CL
    Download Ideal Coordinates CCD File 
    B, C
    		CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.91 Å
    • R-Value Free: 0.229 
    • R-Value Work: 0.178 
    • R-Value Observed: 0.181 
    • Space Group: P 31
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 48.554α = 90
    b = 48.554β = 90
    c = 153.941γ = 120
    Software Package:
    Software NamePurpose
    XDSdata reduction
    PHASERphasing
    PHENIXrefinement

    Structure Validation

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    View more in-depth experimental data

    Entry History & Funding Information

    Deposition Data

    Funding OrganizationLocationGrant Number
    DFGGermany--

    Revision History  (Full details and data files)

    • Version 1.0: 2015-01-14
      Type: Initial release
    • Version 1.1: 2015-01-21
      Changes: Database references
    • Version 1.2: 2015-02-04
      Changes: Database references