5EY0

Crystal structure of CodY from Staphylococcus aureus with GTP and Ile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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:  
    5EY1, 5EY0, 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-sensing transcriptional pleiotropic repressor CodY AB274Staphylococcus aureus subsp. aureus Mu3Mutation(s): 0 
Gene Names: codYSAHV_1245
Find proteins for Q2FZ27 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZ27 
Go to UniProtKB:  Q2FZ27
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
A, B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ILE
Query on ILE

Download Ideal Coordinates CCD File 
A, B
ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GTPKd:  2260000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.894α = 90
b = 76.028β = 90
c = 158.023γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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