2DDC | pdb_00002ddc

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: 
    0.212 (Depositor) 
  • R-Value Work: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 3.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 51.51 kDa 
  • Atom Count: 4,168 
  • Modeled Residue Count: 449 
  • Deposited Residue Count: 450 
  • Unique protein chains: 1

Macromolecules

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|  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
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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:  0.212 (Depositor) 
  • R-Value Work:  0.190 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.629α = 90
b = 119.286β = 120.18
c = 49.068γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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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: 2014-01-15
    Changes: Database references
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-11-13
    Changes: Structure summary
  • Version 3.0: 2026-03-18
    Changes: Polymer sequence