1XMZ

Crystal structure of the dark state of kindling fluorescent protein kfp from anemonia sulcata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kindling Fluorescent Protein from Anemonia sulcata: Dark-State Structure at 1.38 Resolution

Quillin, M.L.Anstrom, D.M.Shu, X.O'Leary, S.Kallio, K.Chudakov, D.M.Remington, S.J.

(2005) Biochemistry 44: 5774-5787

  • DOI: 10.1021/bi047644u

  • PubMed Abstract: 
  • When the nonfluorescent chromoprotein asFP595 from Anemonia sulcata is subjected to sufficiently intense illumination near the absorbance maximum (lambda(abs)(max) = 568 nm), it undergoes a remarkable transition, termed "kindling", to a long-lived fl ...

    When the nonfluorescent chromoprotein asFP595 from Anemonia sulcata is subjected to sufficiently intense illumination near the absorbance maximum (lambda(abs)(max) = 568 nm), it undergoes a remarkable transition, termed "kindling", to a long-lived fluorescent state (lambda(em)(max) = 595 nm). In the dark recovery phase, the kindled state relaxes thermally on a time scale of seconds or can instantly be reverted upon illumination at 450 nm. The kindling phenomenon is enhanced by the Ala143 --> Gly point mutation, which slows the dark recovery time constant to 100 s at room temperature and increases the fluorescence quantum yield. To investigate the chemical nature of the chromophore and the possible role of chromophore isomerization in the kindling phenomenon, we determined the crystal structure of the "kindling fluorescent protein" asFP595-A143G (KFP) in the dark-adapted state at 1.38 A resolution and 100 K. The chromophore, derived from the Met63-Tyr64-Gly65 tripeptide, closely resembles that of the nonfluorescent chromoprotein Rtms5 in that the configuration is trans about the methylene bridge and there is substantial distortion from planarity. Unlike in Rtms5, in the native protein the polypeptide backbone is cleaved between Cys62 and Met63. The size and shape of the chromophore pocket suggest that the cis isomer of the chromophore could also be accommodated. Within the pocket, partially disordered His197 displays two conformations, which may constitute a binary switch that stabilizes different chromophore configurations. The energy barrier for thermal relaxation was found by Arrhenius plot analysis to be approximately 71 kJ/mol, somewhat higher than the value of approximately 55 kJ/mol observed for cis-trans isomerization of a model chromophore in solution.


    Related Citations: 
    • Kindling Fluorescent Proteins for Precise in Vivo Photolabeling
      Chudakov, D.M.,Belousov, V.V.,Zaraisky, A.G.,Novoselov, V.V.,Staroverov, D.B.,Zorov, D.B.,Lukyanov, S.,Lukyanov, K.A.
      (2003) NAT.BIOTECHNOL. 21: 191
    • Synthesis and Properties of the Chromophore of Asulcp Chromoprotein from Anemonia Sulcata
      Yampolsky, I.V.,Remington, S.J.,Potapov, V.K.,Lukyanov, K.A.
      () TO BE PUBLISHED --: --
    • Natural Animal Coloration Can be Determined by a Nonfluorescent Green Fluorescent Protein Homolog
      Lukyanov, K.A.,Fradkov, A.F.,Gurskaya, N.G.,Matz, M.V.,Labas, Y.A.,Savitsky, A.P.,Markelov, M.L.,Zaraisky, A.G.,Zhao, X.,Fang, Y.,Tan, W.,Lukyanov, S.A.
      (2000) J.Biol.Chem. 275: 25879
    • Interconversion of Anthozoa Gfp-Like Fluorescent and Nonfluorescent Proteins by Mutagenesis
      Bulina, M.E.,Chudakov, D.M.,Mudrik, N.N.,Lukyanov, K.A.
      (2002) BMC BIOCHEM. 3: --
    • Alternative Cyclization in Gfp-Like Proteins Family. The Formation and Structure of the Chromophore of a Purple Chromoprotein from Anemonia Sulcata
      Martynov, V.I.,Savitsky, A.P.,Martynova, N.Y.,Savitsky, P.A.,Lukyanov, K.A.,Lukyanov, S.A.
      (2001) J.Biol.Chem. 276: 21012
    • Chromophore Environment Provides Clue to "Kindling Fluorescent Protein" Riddle
      Chudakov, D.M.,Foefanov, A.V.,Mudrik, N.N.,Lukyanov, S.,Lukyanov, K.A.
      (2002) J.Biol.Chem. 278: 7215


    Organizational Affiliation

    Department of Physics, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GFP-like chromoprotein FP595
A, B
243Anemonia sulcataN/A
Find proteins for Q9GZ28 (Anemonia sulcata)
Go to UniProtKB:  Q9GZ28
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NH2
Query on NH2

Download SDF File 
Download CCD File 
A, B
AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYAF
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRK
Query on CRK
A, B
L-PEPTIDE LINKINGC16 H15 N2 O4 SMET, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.139 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.520α = 90.00
b = 125.400β = 90.00
c = 92.750γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXL-97refinement
SCALEPACKdata scaling
EPMRphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance