2H9W

Green fluorescent protein ground states: the influence of a second protonation site near the chromophore


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Green Fluorescent Protein Ground States: The Influence of a Second Protonation Site near the Chromophore.

Bizzarri, R.Nifosi, R.Abbruzzetti, S.Rocchia, W.Guidi, S.Arosio, D.Garau, G.Campanini, B.Grandi, E.Ricci, F.Viappiani, C.Beltram, F.

(2007) Biochemistry 46: 5494-5504

  • DOI: 10.1021/bi602646r

  • PubMed Abstract: 
  • The photophysical properties of most green fluorescent protein mutants (GFPs) are strongly affected by pH. This effect must be carefully taken into account when using GFPs as fluorescent probes or indicators. Usually, the pH-dependence of GFPs is rat ...

    The photophysical properties of most green fluorescent protein mutants (GFPs) are strongly affected by pH. This effect must be carefully taken into account when using GFPs as fluorescent probes or indicators. Usually, the pH-dependence of GFPs is rationalized on the basis of the ionization equilibrium of the chromophore phenol group. Yet many different mutants show spectral behavior that cannot be explained by ionization of this group alone. In this study, we propose a general model of protonation comprising two ionization sites (2S model). Steady-state optical measurements at different pH and temperature and pH-jump relaxation experiments were combined to highlight the thermodynamic and kinetic properties of paradigmatically different GFP variants. Our experiments support the 2S model. For the case of mutants in which E222 is the second protonation site, thermodynamic coupling between this residue's and the chromophore's ionization reactions was demonstrated. In agreement with the 2S model predictions, X-ray analysis of one of these mutants showed the presence of two chromophore populations at high pH.


    Related Citations: 
    • Spectroscopic and Structural Study of the Heterotropic Linkage between Halide and Proton Ion Binding to Gfp Proteins
      Arosio, D.,Garau, G.,Ricci, F.,Nifosi, R.,Beltram, F.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Scuola Normale Superiore-IIT Research Unit, Piazza dei Cavalieri 7 I-56126 Pisa, Italy. r.bizzarri@ sns.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
240Aequorea victoriaMutation(s): 3 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.886α = 90.00
b = 62.933β = 90.00
c = 71.035γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
MOSFLMdata reduction
CCP4model building
CCP4phasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-06-12 
  • Released Date: 2007-04-24 
  • Deposition Author(s): Garau, G.

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-11-12
    Type: Structure summary