5EY1

Crystal structure of CodY from Staphylococcus aureus with GTP and Ile

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Literature

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: 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 ...

    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 chahong@korea.ac.kr.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-sensing transcriptional pleiotropic repressor CodYA, B274Staphylococcus aureus subsp. aureus Mu3Mutation(s): 0 
Gene Names: codY, SAHV_1245
UniProt
Find proteins for Q2FZ27 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZ27 
Go to UniProtKB:  Q2FZ27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FZ27
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
ILE
Query on ILE
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GTP Binding MOAD:  5EY1 Kd: 2.26e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.824α = 90
b = 75.992β = 90
c = 166.301γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-11-24 
  • Released Date: 2016-09-14 
    • Deposition Author(s): Han, A., Hwang, K.Y.

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