4KA9

Crystal structure analysis of single amino acid deletion mutations in EGFP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure.

Arpino, J.A.Reddington, S.C.Halliwell, L.M.Rizkallah, P.J.Jones, D.D.

(2014) Structure 22: 889-898

  • DOI: 10.1016/j.str.2014.03.014

  • PubMed Abstract: 
  • Altering a protein's backbone through amino acid deletion is a common evolutionary mutational mechanism, but is generally ignored during protein engineering primarily because its effect on the folding-structure-function relationship is difficult to p ...

    Altering a protein's backbone through amino acid deletion is a common evolutionary mutational mechanism, but is generally ignored during protein engineering primarily because its effect on the folding-structure-function relationship is difficult to predict. Using directed evolution, enhanced green fluorescent protein (EGFP) was observed to tolerate residue deletion across the breadth of the protein, particularly within short and long loops, helical elements, and at the termini of strands. A variant with G4 removed from a helix (EGFP(G4Δ)) conferred significantly higher cellular fluorescence. Folding analysis revealed that EGFP(G4Δ) retained more structure upon unfolding and refolded with almost 100% efficiency but at the expense of thermodynamic stability. The EGFP(G4Δ) structure revealed that G4 deletion caused a beneficial helical registry shift resulting in a new polar interaction network, which potentially stabilizes a cis proline peptide bond and links secondary structure elements. Thus, deletion mutations and registry shifts can enhance proteins through structural rearrangements not possible by substitution mutations alone.


    Organizational Affiliation

    School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A
238Aequorea victoriaMutation(s): 1 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
A
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.870α = 90.00
b = 66.660β = 108.76
c = 45.290γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2015-11-25
    Type: Database references, Structure summary