3PYP

PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure at 0.85 A resolution of an early protein photocycle intermediate.

Genick, U.K.Soltis, S.M.Kuhn, P.Canestrelli, I.L.Getzoff, E.D.

(1998) Nature 392: 206-209

  • DOI: 10.1038/32462

  • PubMed Abstract: 
  • Protein photosensors from all kingdoms of life use bound organic molecules, known as chromophores, to detect light. A specific double bond within each chromophore is isomerized by light, triggering slower changes in the protein as a whole. The initia ...

    Protein photosensors from all kingdoms of life use bound organic molecules, known as chromophores, to detect light. A specific double bond within each chromophore is isomerized by light, triggering slower changes in the protein as a whole. The initial movements of the chromophore, which can occur in femtoseconds, are tightly constrained by the surrounding protein, making it difficult to see how isomerization can occur, be recognized, and be appropriately converted into a protein-wide structural change and biological signal. Here we report how this dilemma is resolved in the photoactive yellow protein (PYP). We trapped a key early intermediate in the light cycle of PYP at temperatures below -100 degrees C, and determined its structure at better than 1 A resolution. The 4-hydroxycinnamoyl chromophore isomerizes by flipping its thioester linkage with the protein, thus avoiding collisions resulting from large-scale movement of its aromatic ring during the initial light reaction. A protein-to-chromophore hydrogen bond that is present in both the preceding dark state and the subsequent signalling state of the photosensor breaks, forcing one of the hydrogen-bonding partners into a hydrophobic pocket. The isomerized bond is distorted into a conformation resembling that in the transition state. The resultant stored energy is used to drive the PYP light cycle. These results suggest a model for phototransduction, with implications for bacteriorhodopsin, photoactive proteins, PAS domains, and signalling proteins.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, 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: 0.85 Å
  • R-Value Free: 0.155 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 66.224α = 90.00
b = 66.224β = 90.00
c = 40.561γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELX-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-01
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other