3LF4

Crystal Structure of Fluorescent Timer Precursor Blue102


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.808 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Understanding blue-to-red conversion in monomeric fluorescent timers and hydrolytic degradation of their chromophores

Pletnev, S.Subach, F.V.Dauter, Z.Wlodawer, A.Verkhusha, V.V.

(2010) J.Am.Chem.Soc. 132: 2243-2253

  • DOI: 10.1021/ja908418r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fast-FT is a fluorescent timer (FT) engineered from DsRed-like fluorescent protein mCherry. Crystal structures of Fast-FT (chromophore Met66-Tyr67-Gly68) and its precursor with blocked blue-to-red conversion Blue102 (chromophore Leu66-Tyr67-Gly68) ha ...

    Fast-FT is a fluorescent timer (FT) engineered from DsRed-like fluorescent protein mCherry. Crystal structures of Fast-FT (chromophore Met66-Tyr67-Gly68) and its precursor with blocked blue-to-red conversion Blue102 (chromophore Leu66-Tyr67-Gly68) have been determined at the resolution of 1.15 A and 1.81 A, respectively. Structural data suggest that blue-to-red conversion, taking place in Fast-FT and in related FTs, is associated with the oxidation of Calpha2-Cbeta2 bond of Tyr67. Site directed mutagenesis revealed a crucial role of Arg70 and Tyr83 in the delayed oxidation of Calpha2-Cbeta2 bond, introducing the timing factor in maturation of the timer. Substitutions Ser217Ala and Ser217Cys in Fast-FT substantially slow down formation of an intermediate blue chromophore but do not affect much blue-to-red conversion, whereas mutations Arg70Lys or Trp83Leu, having little effect on the blue chromophore formation rate, markedly accelerates formation of the red chromophore. The chromophore of FTs adopts a cis-conformation stabilized by a hydrogen bond between its phenolate oxygen and the side chain hydroxyl of Ser146. In Blue102, a bulky side chain of Ile146 precludes the chromophore from adopting a "cis-like" conformation, blocking its blue-to-red conversion. Both Fast-FT and Blue102 structures revealed hydrolytic degradation of the chromophores. In Fast-FT, chromophore-forming Met66 residue is eliminated from the polypeptide chain, whereas Leu66 in Blue102 is cleaved out from the chromophore, decarboxylated and remains attached to the preceding Phe65. Hydrolysis of the chromophore competes with chromophore maturation and is driven by the same residues that participate in chromophore maturation.


    Organizational Affiliation

    Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, Illinois 60439, USA. pletnevs@mail.nih.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fluorescent Timer Precursor Blue102
A
66Discosoma sp.Mutation(s): 0 
Find proteins for D1MPT3 (Discosoma sp.)
Go to UniProtKB:  D1MPT3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fluorescent Timer Precursor Blue102
B
165Discosoma sp.Mutation(s): 0 
Find proteins for D1MPT3 (Discosoma sp.)
Go to UniProtKB:  D1MPT3
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
LEN
Query on LEN
A
L-peptide COOH carboxy terminusC5 H13 NLEU
0YG
Query on 0YG
B
L-peptide NH3 amino terminusC11 H12 N2 O4TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.808 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.368α = 90.00
b = 42.344β = 127.06
c = 84.964γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
PHENIXrefinement
SERGUIdata collection
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description