Crystal structure of CodY from Bacillus cereus

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

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The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism

Han, A.R.Kang, H.R.Son, J.Kwon, D.H.Kim, S.Lee, W.C.Song, H.K.Song, M.J.Hwang, K.Y.

(2016) Nucleic Acids Res 44: 9483-9493

  • DOI: https://doi.org/10.1093/nar/gkw775
  • Primary Citation of Related Structures:  
    5EY0, 5EY1, 5EY2

  • PubMed Abstract: 

    GTP and branched-chain amino acids (BCAAs) are metabolic sensors that are indispensable for the determination of the metabolic status of cells. However, their molecular sensing mechanism remains unclear. CodY is a unique global transcription regulator that recognizes GTP and BCAAs as specific signals and affects expression of more than 100 genes associated with metabolism. Herein, we report the first crystal structures of the full-length CodY complex with sensing molecules and describe their functional states. We observed two different oligomeric states of CodY: a dimeric complex of CodY from Staphylococcus aureus with the two metabolites GTP and isoleucine, and a tetrameric form (apo) of CodY from Bacillus cereus Notably, the tetrameric state shows in an auto-inhibitory manner by blocking the GTP-binding site, whereas the binding sites of GTP and isoleucine are clearly visible in the dimeric state. The GTP is located at a hinge site between the long helical region and the metabolite-binding site. Together, data from structural and electrophoretic mobility shift assay analyses improve understanding of how CodY senses GTP and operates as a DNA-binding protein and a pleiotropic transcription regulator.

  • Organizational Affiliation

    Department of Biosystems & Biotechnology, Korea University, Anam-dong, Seoungbuk-gu, Seoul 136-713, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-sensing transcriptional pleiotropic repressor CodYA,
C [auth D],
D [auth C]
276Bacillus cereus ATCC 14579Mutation(s): 0 
Gene Names: codYBC_3826
Find proteins for Q819X8 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711))
Explore Q819X8 
Go to UniProtKB:  Q819X8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ819X8
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
C [auth D],
D [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.066α = 90
b = 132.066β = 90
c = 223.082γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2016-11-16
    Changes: Database references
  • Version 1.3: 2020-02-19
    Changes: Data collection, Database references, Derived calculations