4ZBL

Phototoxic fluorescent protein mKillerOrange


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Phototoxic Orange Fluorescent Proteins with a Tryptophan-Based Chromophore.

Pletneva, N.V.Pletnev, V.Z.Sarkisyan, K.S.Gorbachev, D.A.Egorov, E.S.Mishin, A.S.Lukyanov, K.A.Dauter, Z.Pletnev, S.

(2015) Plos One 10: e0145740-e0145740

  • DOI: 10.1371/journal.pone.0145740
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phototoxic fluorescent proteins represent a sparse group of genetically encoded photosensitizers that could be used for precise light-induced inactivation of target proteins, DNA damage, and cell killing. Only two such GFP-based fluorescent proteins ...

    Phototoxic fluorescent proteins represent a sparse group of genetically encoded photosensitizers that could be used for precise light-induced inactivation of target proteins, DNA damage, and cell killing. Only two such GFP-based fluorescent proteins (FPs), KillerRed and its monomeric variant SuperNova, were described up to date. Here, we present a crystallographic study of their two orange successors, dimeric KillerOrange and monomeric mKillerOrange, at 1.81 and 1.57 Å resolution, respectively. They are the first orange-emitting protein photosensitizers with a tryptophan-based chromophore (Gln65-Trp66-Gly67). Same as their red progenitors, both orange photosensitizers have a water-filled channel connecting the chromophore to the β-barrel exterior and enabling transport of ROS. In both proteins, Trp66 of the chromophore adopts an unusual trans-cis conformation stabilized by H-bond with the nearby Gln159. This trans-cis conformation along with the water channel was shown to be a key structural feature providing bright orange emission and phototoxicity of both examined orange photosensitizers.


    Related Citations: 
    • Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed.
      Pletnev, S.,Gurskaya, N.G.,Pletneva, N.V.,Lukyanov, K.A.,Chudakov, D.M.,Martynov, V.I.,Popov, V.O.,Kovalchuk, M.V.,Wlodawer, A.,Dauter, Z.,Pletnev, V.
      (2009) J. Biol. Chem. 284: 32028


    Organizational Affiliation

    Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosesitizer mKillerOrange
A
240Anthomedusae sp. DC-2005Mutation(s): 0 
Find proteins for Q2TCH5 (Anthomedusae sp. DC-2005)
Go to UniProtKB:  Q2TCH5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4M9
Query on 4M9
A
NON-POLYMERC18 H17 N5 O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 64.160α = 90.00
b = 64.160β = 90.00
c = 47.350γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation14-14-00281

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references
  • Version 1.2: 2017-11-29
    Type: Database references
  • Version 1.3: 2018-08-29
    Type: Data collection, Database references