4B9O

The PR0 Photocycle Intermediate of Photoactive Yellow Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Watching a Signaling Protein Function in Real Time Via 100-Ps Time-Resolved Laue Crystallography

Schotte, F.Cho, H.S.Kaila, V.R.I.Kamikubo, H.Dashdorj, N.Henry, E.R.Graber, T.J.Henning, R.Wulff, M.Hummer, G.Kataoka, M.Anfinrud, P.A.

(2012) Proc.Natl.Acad.Sci.USA 109: 19256

  • DOI: 10.1073/pnas.1210938109
  • Primary Citation of Related Structures:  4BBT, 4BBU, 4BBV

  • PubMed Abstract: 
  • To understand how signaling proteins function, it is crucial to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required ...

    To understand how signaling proteins function, it is crucial to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required to characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, and have used this capability to track the reversible photocycle of photoactive yellow protein (PYP) following trans-to-cis photoisomerization of its p-coumaric acid (pCA) chromophore over 10 decades of time. The first of four major intermediates characterized in this study is highly contorted, with the pCA carbonyl rotated nearly 90° out of the plane of the phenolate. A hydrogen bond between the pCA carbonyl and the Cys69 backbone constrains the chromophore in this unusual twisted conformation. Density functional theory calculations confirm that this structure is chemically plausible and corresponds to a strained cis intermediate. This unique structure is short-lived (∼600 ps), has not been observed in prior cryocrystallography experiments, and is the progenitor of intermediates characterized in previous nanosecond time-resolved Laue crystallography studies. The structural transitions unveiled during the PYP photocycle include trans/cis isomerization, the breaking and making of hydrogen bonds, formation/relaxation of strain, and gated water penetration into the interior of the protein. This mechanistically detailed, near-atomic resolution description of the complete PYP photocycle provides a framework for understanding signal transduction in proteins, and for assessing and validating theoretical/computational approaches in protein biophysics.


    Organizational Affiliation

    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOACTIVE YELLOW PROTEIN
A
125Halorhodospira halophilaGene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Go to UniProtKB:  P16113
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4
Query on HC4

Download SDF File 
Download CCD File 
A
4'-HYDROXYCINNAMIC ACID
PARA-COUMARIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.221 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 66.833α = 90.00
b = 66.833β = 90.00
c = 40.947γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-11-28
    Type: Database references
  • Version 1.2: 2012-12-05
    Type: Database references