2DDD

Unique behavior of a histidine responsible for an engineered green-to-red photoconversion process


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.175 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The E1 mechanism in photo-induced beta-elimination reactions for green-to-red conversion of fluorescent proteins

Tsutsui, H.Shimizu, H.Mizuno, H.Nukina, N.Furuta, T.Miyawaki, A.

(2009) Chem Biol 16: 1140-1147

  • DOI: https://doi.org/10.1016/j.chembiol.2009.10.010
  • Primary Citation of Related Structures:  
    2DDC, 2DDD

  • PubMed Abstract: 

    KikGR is a fluorescent protein engineered to display green-to-red photoconvertibility that is induced by irradiation with ultraviolet or violet light. Similar to Kaede and EosFP, two naturally occurring photoconvertible proteins, KikGR contains a His(62)-Tyr(63)-Gly(64) tripeptide sequence, which forms a green chromophore that can be photoconverted to a red one via formal beta-elimination and subsequent extension of a pi-conjugated system. Using a crystallizable variant of KikGR, we determined the structures of both the green and red state at 1.55 A resolution. The double bond between His(62)-C(alpha) and His(62)-C(beta) in the red chromophore is in a cis configuration, indicating that rotation along the His(62) C(alpha)-C(beta) bond occurs following cleavage of the His(62) N(alpha)-C(alpha) bond. This structural rearrangement provides evidence that the beta-elimination reaction governing the green-to-red photoconversion of KikGR follows an E1 (elimination, unimolecular) mechanism.


  • Organizational Affiliation

    Brain Science Institute, RIKEN, Hirosawa, Wako-city, Saitama, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
photoconvertible fluorescent protein
A, B
225Dipsastraea favusMutation(s): 6 
UniProt
Find proteins for Q53UG8 (Dipsastraea favus)
Explore Q53UG8 
Go to UniProtKB:  Q53UG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53UG8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CR8
Query on CR8
A, B
L-PEPTIDE LINKINGC17 H16 N5 O4HIS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.837α = 90
b = 118.41β = 119.96
c = 48.856γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations