4DXM

Crystal Structure of an ancestral GFP-like protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins.

Kim, H.Zou, T.Modi, C.Dorner, K.Grunkemeyer, T.J.Chen, L.Fromme, R.Matz, M.V.Ozkan, S.B.Wachter, R.M.

(2015) Structure 23: 34-43

  • DOI: 10.1016/j.str.2014.11.011
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In proteins, functional divergence involves mutations that modify structure and dynamics. Here we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, cataly ...

    In proteins, functional divergence involves mutations that modify structure and dynamics. Here we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, catalytic group rearrangements, or changes in subunit assembly. Crystallographic structures were determined for several reconstructed ancestral proteins belonging to a GFP class frequently employed in superresolution microscopy. Their chain flexibility was analyzed using molecular dynamics and perturbation response scanning. The green-to-red photoconvertible phenotype appears to have arisen from a common green ancestor by migration of a knob-like anchoring region away from the active site diagonally across the β barrel fold. The allosterically coupled mutational sites provide active site conformational mobility via epistasis. We propose that light-induced chromophore twisting is enhanced in a reverse-protonated subpopulation, activating internal acid-base chemistry and backbone cleavage to enlarge the chromophore. Dynamics-driven hinge migration may represent a more general platform for the evolution of novel enzyme activities.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ 85287, USA. Electronic address: rwachter@asu.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GREEN FLUORESCENT PROTEINA, B, C, D229synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR8
Query on CR8
A,B,C,DL-PEPTIDE LINKINGC17 H16 N5 O4HIS,TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.28α = 90
b = 92.71β = 93.18
c = 89.06γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references