4DXP

Crystal Structure of a reconstructed Kaede-type Red Fluorescent Protein, LEA X121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: https://doi.org/10.1016/j.str.2014.11.011
  • Primary Citation of Related Structures:  
    4DXI, 4DXM, 4DXO, 4DXP

  • 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, 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LEA X121 GFP-LIKE PROTEINS228synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CR8
Query on CR8
A
L-PEPTIDE LINKINGC17 H16 N5 O4HIS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.04α = 90
b = 79.18β = 90
c = 118.04γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations