2HCG

Structure of S65T Y66F GFP variant after cyclization, carbon-carbon bond cleavage, and oxygen incorporation reactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Case of the Missing Ring: Radical Cleavage of a Carbon-Carbon Bond and Implications for GFP Chromophore Biosynthesis

Barondeau, D.P.Kassmann, C.J.Tainer, J.A.Getzoff, E.D.

(2007) J.Am.Chem.Soc. 129: 3118-3126

  • DOI: 10.1021/ja063983u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The green fluorescent protein (GFP) creates its fluorophore by promoting spontaneous peptide backbone cyclization and amino acid oxidation chemistry on its own Ser65, Tyr66, Gly67 tripeptide sequence. Here we use high-resolution crystallography and m ...

    The green fluorescent protein (GFP) creates its fluorophore by promoting spontaneous peptide backbone cyclization and amino acid oxidation chemistry on its own Ser65, Tyr66, Gly67 tripeptide sequence. Here we use high-resolution crystallography and mutational analyses to characterize GFP variants that undergo backbone cyclization followed by either anticipated chromophore synthesis via Y66F Calpha-Cbeta double-bond formation or unprecedented loss of a Y66F benzyl moiety via Calpha-Cbeta bond cleavage. We discovered a Y66F cleavage variant that subsequently incorporates an oxygen atom, likely from molecular oxygen, at the Y66 Calpha position. The post-translational products identified from these Y66F GFP structures support a common intermediate that partitions between Calpha-Cbeta oxidation and homolytic cleavage pathways. Our data indicate that Glu222 is the branchpoint control for this partitioning step and also influences subsequent oxygen incorporation reactions. From these results, we propose mechanisms for Y66F Calpha-Cbeta cleavage, oxygen incorporation, and chromophore biosynthesis with shared features that include radical chemistry. By revealing how GFP and RFP protein environments steer chemistry to favor fluorophore biosynthesis and disfavor alternative reactivity, we identify strategies for protein design. The proposed, common, one-electron oxidized, radical intermediate for post-translation modifications in the GFP family has general implications for how proteins drive and control spontaneous post-translational chemical modifications in the absence of metal ions.


    Organizational Affiliation

    Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
239Aequorea victoriaMutation(s): 4 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
C99
Query on C99
A
L-PEPTIDE LINKINGC8 H13 N3 O6THR, PHE, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.132α = 90.00
b = 62.501β = 90.00
c = 71.187γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ADSCdata collection
AMoREphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance