5EXC

Photoconverted red fluorescent protein DendRFP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms.

Pletneva, N.V.Pletnev, S.Pakhomov, A.A.Chertkova, R.V.Martynov, V.I.Muslinkina, L.Dauter, Z.Pletnev, V.Z.

(2016) Acta Crystallogr D Struct Biol 72: 922-932

  • DOI: 10.1107/S205979831601038X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The fluorescent protein from Dendronephthya sp. (DendFP) is a member of the Kaede-like group of photoconvertible fluorescent proteins with a His62-Tyr63-Gly64 chromophore-forming sequence. Upon irradiation with UV and blue light, the fluorescence of ...

    The fluorescent protein from Dendronephthya sp. (DendFP) is a member of the Kaede-like group of photoconvertible fluorescent proteins with a His62-Tyr63-Gly64 chromophore-forming sequence. Upon irradiation with UV and blue light, the fluorescence of DendFP irreversibly changes from green (506 nm) to red (578 nm). The photoconversion is accompanied by cleavage of the peptide backbone at the C(α)-N bond of His62 and the formation of a terminal carboxamide group at the preceding Leu61. The resulting double C(α)=C(β) bond in His62 extends the conjugation of the chromophore π system to include imidazole, providing the red fluorescence. Here, the three-dimensional structures of native green and photoconverted red forms of DendFP determined at 1.81 and 2.14 Å resolution, respectively, are reported. This is the first structure of photoconverted red DendFP to be reported to date. The structure-based mutagenesis of DendFP revealed an important role of positions 142 and 193: replacement of the original Ser142 and His193 caused a moderate red shift in the fluorescence and a considerable increase in the photoconversion rate. It was demonstrated that hydrogen bonding of the chromophore to the Gln116 and Ser105 cluster is crucial for variation of the photoconversion rate. The single replacement Gln116Asn disrupts the hydrogen bonding of Gln116 to the chromophore, resulting in a 30-fold decrease in the photoconversion rate, which was partially restored by a further Ser105Asn replacement.


    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
Green fluorescent protein
A, B, C, D, E, F, G, H
62Dendronephthya sp. SSAL-2002Mutation(s): 0 
Find proteins for Q8T6U0 (Dendronephthya sp. SSAL-2002)
Go to UniProtKB:  Q8T6U0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
I, J, K, L, M, N, O, P
172Dendronephthya sp. SSAL-2002Mutation(s): 0 
Find proteins for Q8T6U0 (Dendronephthya sp. SSAL-2002)
Go to UniProtKB:  Q8T6U0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
E, G, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
E, F, G, H, N, O, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NLW
Query on NLW
A, B, C, D, E, F, G, H
L-peptide linkingC6 H14 N2 OLeu
RC7
Query on RC7
I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC17 H18 N4 O4HIS,TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.195 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.423α = 89.88
b = 69.521β = 89.94
c = 124.481γ = 65.57
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2016-08-17
    Type: Database references