3UME

Structure of pB intermediate of Photoactive yellow protein (PYP) at pH 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

pH Dependence of the Photoactive Yellow Protein Photocycle Investigated by Time-Resolved Crystallography.

Tripathi, S.Srajer, V.Purwar, N.Henning, R.Schmidt, M.

(2012) Biophys.J. 102: 325-332

  • DOI: 10.1016/j.bpj.2011.11.4021
  • Primary Citation of Related Structures:  3UMD

  • PubMed Abstract: 
  • Visualizing the three-dimensional structures of a protein during its biological activity is key to understanding its mechanism. In general, protein structure and function are pH-dependent. Changing the pH provides new insights into the mechanisms tha ...

    Visualizing the three-dimensional structures of a protein during its biological activity is key to understanding its mechanism. In general, protein structure and function are pH-dependent. Changing the pH provides new insights into the mechanisms that are involved in protein activity. Photoactive yellow protein (PYP) is a signaling protein that serves as an ideal model for time-dependent studies on light-activated proteins. Its photocycle is studied extensively under different pH conditions. However, the structures of the intermediates remain unknown until time-resolved crystallography is employed. With the newest beamline developments, a comprehensive time series of Laue data can now be collected from a single protein crystal. This allows us to vary the pH. Here we present the first structure, to our knowledge, of a short-lived protein-inhibitor complex formed in the pB state of the PYP photocycle at pH 4. A water molecule that is transiently stabilized in the chromophore active site prevents the relaxation of the chromophore back to the trans configuration. As a result, the dark-state recovery is slowed down dramatically. At pH 9, PYP stops cycling through the pB state altogether. The electrostatic environment in the chromophore-binding site is the likely reason for this altered kinetics at different pH values.


    Organizational Affiliation

    University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 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: 1.8 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.120 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 66.900α = 90.00
b = 66.900β = 90.00
c = 40.800γ = 120.00
Software Package:
Software NamePurpose
Precognitiondata reduction
XFITdata reduction
CNSrefinement
Epinormdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description