5LOE

Structure of full length Cody from Bacillus subtilis in complex with Ile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Branched-chain Amino Acid and GTP-sensing Global Regulator, CodY, from Bacillus subtilis.

Levdikov, V.M.Blagova, E.Young, V.L.Belitsky, B.R.Lebedev, A.Sonenshein, A.L.Wilkinson, A.J.

(2017) J. Biol. Chem. 292: 2714-2728

  • DOI: 10.1074/jbc.M116.754309
  • Primary Citation of Related Structures:  
  • Also Cited By: 5N0L

  • PubMed Abstract: 
  • CodY is a branched-chain amino acid (BCAA) and GTP sensor and a global regulator of transcription in low G + C Gram-positive bacteria. It controls the expression of over 100 genes and operons, principally by repressing during growth genes whose produ ...

    CodY is a branched-chain amino acid (BCAA) and GTP sensor and a global regulator of transcription in low G + C Gram-positive bacteria. It controls the expression of over 100 genes and operons, principally by repressing during growth genes whose products are required for adaptations to nutrient limitation. However, the mechanism by which BCAA binding regulates transcriptional changes is not clear. It is known that CodY consists of a GAF (cGMP-stimulated phosphodiesterases, adenylate cyclases, FhlA) domain that binds BCAAs and a winged helix-turn-helix (wHTH) domain that binds to DNA, but the way in which these domains interact and the structural basis of the BCAA dependence of this interaction are unknown. To gain new insights, we determined the crystal structure of unliganded CodY from Bacillus subtilis revealing a 10-turn α-helix linking otherwise discrete GAF and wHTH domains. The structure of CodY in complex with isoleucine revealed a reorganized GAF domain. In both complexes CodY was tetrameric. Size exclusion chromatography with multiangle laser light scattering (SEC-MALLS) experiments showed that CodY is a dimer at concentrations found in bacterial cells. Comparison of structures of dimers of unliganded CodY and CodY-Ile derived from the tetramers showed a splaying of the wHTH domains when Ile was bound; splaying is likely to account for the increased affinity of Ile-bound CodY for DNA. Electrophoretic mobility shift and SEC-MALLS analyses of CodY binding to 19-36-bp operator fragments are consistent with isoleucine-dependent binding of two CodY dimers per duplex. The implications of these observations for effector control of CodY activity 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
    • Structural rearrangement accompanying ligand binding in the GAF domain of CodY from Bacillus subtilis.
      Levdikov, V.M.,Blagova, E.,Colledge, V.L.,Lebedev, A.A.,Williamson, D.C.,Sonenshein, A.L.,Wilkinson, A.J.
      (2009) J. Mol. Biol. 390: 1007


    Organizational Affiliation

    From the Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-sensing transcriptional pleiotropic repressor CodY
A, B, C, D
262Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: codY
Find proteins for P39779 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39779
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ILE
Query on ILE

Download SDF File 
Download CCD File 
A, B, C, D
ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 134.690α = 90.00
b = 158.877β = 90.00
c = 55.412γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBBS/B1213X
Wellcome TrustUnited Kingdom082829/Z/07/Z
NIGMSUnited StatesGM042219

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-01
    Type: Database references
  • Version 1.2: 2017-08-30
    Type: Author supporting evidence
  • Version 1.3: 2018-05-09
    Type: Data collection