1NWZ

PYP Ultra-high resolution structure of a Bacterial Photoreceptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.82 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 

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This is version 1.2 of the entry. See complete history


Literature

Anticipatory active-site motions and chromophore distortions prime photoreceptor PYP for light activation

Getzoff, E.D.Gutwin, K.N.Genick, U.K.

(2003) Nat Struct Biol 10: 663-668

  • DOI: 10.1038/nsb958
  • Primary Citation of Related Structures:  
    1NWZ

  • PubMed Abstract: 
  • Protein photoreceptors use small-molecule cofactors called chromophores to detect light. Only under the influence of the receptors' active sites do these chromophores adopt spectral and photochemical properties that suit the receptors' functional requirements ...

    Protein photoreceptors use small-molecule cofactors called chromophores to detect light. Only under the influence of the receptors' active sites do these chromophores adopt spectral and photochemical properties that suit the receptors' functional requirements. This protein-induced change in chromophore properties is called photochemical tuning and is a prime example for the general--but poorly understood--process of chemical tuning through which proteins shape the reactivity of their active-site groups. Here we report the 0.82-A resolution X-ray structure of the bacterial light receptor photoactive yellow protein (PYP). The unusually precise structure reveals deviations from expected molecular geometries and anisotropic atomic displacements in the PYP active site. Our analysis of these deviations points directly to the intramolecular forces and active-site dynamics that tune the properties of PYP's chromophore to absorb blue light, suppress fluorescence, and favor the required light-driven double-bond isomerization.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA. edg@scripps.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photoactive yellow proteinA125Halorhodospira halophilaMutation(s): 0 
Gene Names: pyp
UniProt
Find proteins for P16113 (Halorhodospira halophila)
Explore P16113 
Go to UniProtKB:  P16113
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4 (Subject of Investigation/LOI)
Query on HC4

Download Ideal Coordinates CCD File 
B [auth A]4'-HYDROXYCINNAMIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.82 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.699α = 90
b = 65.699β = 90
c = 40.239γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
XFITdata reduction
SHELXL-97refinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance