1UWP

Initial Events in the Photocycle of Photoactive Yellow Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Initial Events in the Photocycle of Photoactive Yellow Protein

Kort, R.Hellingwerf, K.J.Ravelli, R.B.G.

(2004) J.Biol.Chem. 279: 26417

  • DOI: 10.1074/jbc.M311961200
  • Primary Citation of Related Structures:  1UWN

  • PubMed Abstract: 
  • The light-induced isomerization of a double bond is the key event that allows the conversion of light energy into a structural change in photoactive proteins for many light-mediated biological processes, such as vision, photosynthesis, photomorphogen ...

    The light-induced isomerization of a double bond is the key event that allows the conversion of light energy into a structural change in photoactive proteins for many light-mediated biological processes, such as vision, photosynthesis, photomorphogenesis, and photo movement. Cofactors such as retinals, linear tetrapyrroles, and 4-hydroxy-cinnamic acid have been selected by nature that provide the essential double bond to transduce the light signal into a conformational change and eventually, a physiological response. Here we report the first events after light excitation of the latter chromophore, containing a single ethylene double bond, in a low temperature crystallographic study of the photoactive yellow protein. We measured experimental phases to overcome possible model bias, corrected for minimized radiation damage, and measured absorption spectra of crystals to analyze the photoproducts formed. The data show a mechanism for the light activation of photoactive yellow protein, where the energy to drive the remainder of the conformational changes is stored in a slightly strained but fully cis-chromophore configuration. In addition, our data indicate a role for backbone rearrangements during the very early structural events.


    Related Citations: 
    • Characterization of Photocycle Intermediates in Crystalline Photoactive Yellow Protein
      Kort, R.,Ravelli, R.B.G.,Schotte, F.,Bourgeois, D.,Crielaard, W.,Hellingwerf, K.J.,Wulff, M.
      (2003) Photochem.Photobiol. 78: 131


    Organizational Affiliation

    Laboratory for Microbiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands. rkort@science.uva.nl




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOACTIVE YELLOW PROTEIN
X
125Halorhodospira halophilaGene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Go to UniProtKB:  P16113
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HC4
Query on HC4

Download SDF File 
Download CCD File 
X
4'-HYDROXYCINNAMIC ACID
PARA-COUMARIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
X
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.136 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 65.922α = 90.00
b = 65.922β = 90.00
c = 40.584γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SHARPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Version format compliance