5BTT

Switching GFP fluorescence using genetically encoded phenyl azide chemistry through two different non-native post-translational modifications routes at the same position.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for functional switching of GFP by two disparate non-native post-translational modifications of a phenyl azide reaction handle.

Hartley, A.M.Worthy, H.L.Reddington, S.C.Rizkallah, P.J.Jones, D.D.

(2016) Chem Sci 7: 6484-6491

  • DOI: 10.1039/c6sc00944a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Through the genetic incorporation of a single phenyl azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro an ...

    Through the genetic incorporation of a single phenyl azide group into superfolder GFP (sfGFP) at residue 148 we provide a molecular description of how this highly versatile chemical handle can be used to positively switch protein function in vitro and in vivo via either photochemistry or bioconjugation. Replacement of H148 with p-azido-l-phenylalanine (azF) blue shifts the major excitation peak ∼90 nm by disrupting the H-bond and proton transfer network that defines the chromophore charged state. Bioorthogonal click modification with a simple dibenzylcyclooctyne or UV irradiation shifts the neutral-anionic chromophore equilibrium, switching fluorescence to the optimal ∼490 nm excitation. Click modification also improved quantum yield over both the unmodified and original protein. Crystal structures of both the click modified and photochemically converted forms show that functional switching is due to local conformational changes that optimise the interaction networks surrounding the chromophore. Crystal structure and mass spectrometry studies of the irradiated protein suggest that the phenyl azide converts to a dehydroazepine and/or an azepinone. Thus, protein embedded phenyl azides can be used beyond simple photocrosslinkers and passive conjugation handles, and mimic many natural post-translational modifications: modulation though changes in interaction networks.


    Organizational Affiliation

    School of Biosciences , Cardiff University , Cardiff , UK . Email: jonesdd@cardiff.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
230Aequorea victoriaMutation(s): 0 
Gene Names: gfp
Find proteins for A0A059PIQ0 (Aequorea victoria)
Go to UniProtKB:  A0A059PIQ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
B
230Aequorea victoriaMutation(s): 0 
Gene Names: gfp
Find proteins for A0A059PIQ0 (Aequorea victoria)
Go to UniProtKB:  A0A059PIQ0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
4V0
Query on 4V0
A
NON-POLYMERC9 H12 N2 O2

--

CRO
Query on CRO
A, B
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
HOX
Query on HOX
B
L-PEPTIDE LINKINGC9 H12 N2 O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.140α = 90.00
b = 135.140β = 90.00
c = 69.560γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2017-05-10
    Type: Database references