Crystal structure of the GntR-HutC family member YvoA from Bacillus subtilis

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.205 

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Insight Into the Induction Mechanism of the Gntr/Hutc Bacterial Transcription Regulator Yvoa

Resch, M.Schiltz, E.Titgemeyer, F.Muller, Y.A.

(2010) Nucleic Acids Res 38: 2485

  • DOI: https://doi.org/10.1093/nar/gkp1191
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    YvoA is a GntR/HutC transcription regulator from Bacillus subtilis implicated in the regulation of genes from the N-acetylglucosamine-degrading pathway. Its 2.4-A crystal structure reveals a homodimeric assembly with each monomer displaying a two-domain fold. The C-terminal domain, which binds the effector N-acetylglucosamine-6-phosphate, adopts a chorismate lyase fold, whereas the N-terminal domain contains a winged helix-turn-helix DNA-binding domain. Isothermal titration calorimetry and site-directed mutagenesis revealed that the effector-binding site in YvoA coincides with the active site of related chorismate lyase from Escherichia coli. The characterization of the DNA- and effector-binding properties of two disulfide-bridged mutants that lock YvoA in two distinct conformational states provides for the first time detailed insight into the allosteric mechanism through which effector binding modulates DNA binding and, thereby regulates transcription in a representative GntR/HutC family member. Central to this allosteric coupling mechanism is a loop-to-helix transition with the dipole of the newly formed helix pointing toward the phosphate of the effector. This transition goes in hand with the emergence of internal symmetry in the effector-binding domain and, in addition, leads to a 122 degrees rotation of the DNA-binding domains that is best described as a jumping-jack-like motion.

  • Organizational Affiliation

    Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, D-91052 Erlangen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
243Bacillus subtilisMutation(s): 0 
Find proteins for O34817 (Bacillus subtilis (strain 168))
Explore O34817 
Go to UniProtKB:  O34817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth B]
N [auth B]
O [auth C]
K [auth A],
L [auth A],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth E],
T [auth F],
U [auth F],
V [auth G],
W [auth G],
X [auth I],
Y [auth I]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.41α = 90
b = 137.08β = 94.97
c = 120.19γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance