3VE3

Structure of IT Intermediate from time-resolved laue crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.291 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography

Jung, Y.O.Lee, J.H.Kim, J.Schmidt, M.Moffat, K.Srajer, V.Ihee, H.

(2013) Nat Chem 5: 212-220

  • DOI: 10.1038/nchem.1565
  • Primary Citation of Related Structures:  
    4I38, 4I39, 4I3I, 4I3J, 4I3A, 4HY8, 3VE3, 3VE4

  • PubMed Abstract: 
  • Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-c ...

    Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-conserving mechanism in which highly choreographed atomic motions are expected, the details of which have not yet been observed directly. Here we employ time-resolved X-ray crystallography to visualize structurally the isomerization of the p-coumaric acid chromophore in photoactive yellow protein with a time resolution of 100 ps and a spatial resolution of 1.6 Å. The structure of the earliest intermediate (I(T)) resembles a highly strained transition state in which the torsion angle is located halfway between the trans- and cis-isomers. The reaction trajectory of I(T) bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue through E46Q mutation, which switches off the bicycle-pedal pathway.


    Organizational Affiliation

    Center for Nanomaterials and Chemical Reactions, Institute for Basic Science, Daejeon 305-701, Republic of Korea.



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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.291 
  • R-Value Observed: 0.239 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.833α = 90
b = 66.833β = 90
c = 40.947γ = 120
Software Package:
Software NamePurpose
LaueViewdata scaling
SHELXL-97refinement
LaueViewdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-01-07 
  • Released Date: 2013-03-20 
  • Deposition Author(s): Ihee, H., Jung, Y.O.

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Structure summary
  • Version 1.2: 2017-11-08
    Changes: Refinement description