2GX5

N-terminal GAF domain of transcriptional pleiotropic repressor CodY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria.

Levdikov, V.M.Blagova, E.Joseph, P.Sonenshein, A.L.Wilkinson, A.J.

(2006) J Biol Chem 281: 11366-11373

  • DOI: 10.1074/jbc.M513015200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • CodY is a global regulator of transcription in gram-positive bacteria. It represses during growth genes required for adaptation to nutrient limitation, including virulence genes in some human pathogens. CodY activity is regulated by GTP and branched ...

    CodY is a global regulator of transcription in gram-positive bacteria. It represses during growth genes required for adaptation to nutrient limitation, including virulence genes in some human pathogens. CodY activity is regulated by GTP and branched chain amino acids, metabolites whose intracellular concentrations drop as cells enter stationary phase. Although CodY has a highly conserved sequence, it has no significant similarity to proteins of known structure. Here we report crystal structures of two fragments of CodY from Bacillus subtilis that clearly constitute its cofactor and DNA binding domains and reveal that CodY is a chimera of previously observed folding units. The N-terminal cofactor-binding fragment adopts a fold reminiscent of the GAF domains found in cyclic nucleotide phosphodiesterases and adenylate cyclases. It is a dimer stabilized by an intermolecular six alpha-helical bundle that buries an extensive apolar surface rich in residues invariant in CodY orthologues. The branched chain amino acid ligands reside in hydrophobic pockets of each monomer distal to the dimer-forming surface. The structure of the C-terminal DNA binding domain belongs to the winged helix-turn-helix family. The implications of the structure for DNA binding by CodY and its control by cofactor binding are discussed.


    Related Citations: 
    • The Structure of CodY, a GTP- and Isoleucine-responsive Regulator of Stationary Phase and Virulence in Gram-positive Bacteria
      Levdikov, V.M., Blagova, E., Joseph, P., Sonenshein, A.L., Wilkinson, A.J.
      (2006) J Biol Chem 281: 11366
    • Crystallization of the GTP-dependent transcriptional regulator CodY from Bacillus subtilis
      Blagova, E.V., Levdikov, V.M., Tachikawa, K., Sonenshein, A.L., Wilkinson, A.J.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 155

    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-sensing transcriptional pleiotropic repressor codYA, B, C, D170Bacillus subtilisMutation(s): 0 
Gene Names: codY
Find proteins for P39779 (Bacillus subtilis (strain 168))
Explore P39779 
Go to UniProtKB:  P39779
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCG
Query on PCG

Download CCD File 
C
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
 Ligand Interaction
P6G
Query on P6G

Download CCD File 
C
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.207α = 90
b = 90.207β = 90
c = 205.634γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance