1XQM

Variations on the GFP chromophore scaffold: A fragmented 5-membered heterocycle revealed in the 2.1A crystal structure of a non-fluorescent chromoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Variations on the GFP chromophore: A polypeptide fragmentation within the chromophore revealed in the 2.1-A crystal structure of a nonfluorescent chromoprotein from Anemonia sulcata

Wilmann, P.G.Petersen, J.Devenish, R.J.Prescott, M.Rossjohn, J.

(2005) J.Biol.Chem. 280: 2401-2404

  • DOI: 10.1074/jbc.C400484200

  • PubMed Abstract: 
  • We have determined to 2.1 A resolution the crystal structure of a dark state, kindling fluorescent protein isolated from the sea anemone, Anemonia sulcata. The chromophore sequence Met(63)-Tyr(64)-Gly(65) of the A. sulcata chromoprotein was previousl ...

    We have determined to 2.1 A resolution the crystal structure of a dark state, kindling fluorescent protein isolated from the sea anemone, Anemonia sulcata. The chromophore sequence Met(63)-Tyr(64)-Gly(65) of the A. sulcata chromoprotein was previously proposed to comprise a 6-membered pyrazine-type heterocycle (Martynov, V. I., Savitsky, A. P., Martynova, N. Y., Savitsky, P. A., Lukyanov, K. A., and Lukyanov, S. A. (2001) J. Biol. Chem. 276, 21012-21016). However, our crystallographic data revealed the chromophore to comprise a 5-membered p-hydroxybenzylideneimidazolinone moiety that adopts a non-coplanar trans conformation within the interior of the GFP beta-can fold. Unexpectedly, fragmentation of the polypeptide was found to occur within the chromophore moiety, at the bond between Cys(62C) and Met(63N1.) Our structural data reveal that fragmentation of the chromophore represents an intrinsic, autocatalytic step toward the formation of the mature chromophore within the specific GFP-like proteins.


    Organizational Affiliation

    Protein Crystallography Unit, Monash Centre for Synchrotron Science.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
kindling fluorescent protein
A
232Anemonia sulcataMutation(s): 0 
Find proteins for Q9GZ28 (Anemonia sulcata)
Go to UniProtKB:  Q9GZ28
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CH6
Query on CH6
A
L-PEPTIDE LINKINGC16 H19 N3 O4 SMET, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.214 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 112.482α = 90.00
b = 112.482β = 90.00
c = 96.906γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-16
    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