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

Nat Chem. 2013 Mar;5(3):212-20. doi: 10.1038/nchem.1565. Epub 2013 Feb 3.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Crystallography, X-Ray / methods
  • Isomerism
  • Models, Molecular
  • Photoreceptors, Microbial / chemistry*
  • Protein Conformation
  • Structure-Activity Relationship


  • Bacterial Proteins
  • Photoreceptors, Microbial
  • photoactive yellow protein, Bacteria

Associated data

  • PDB/3VE3
  • PDB/3VE4
  • PDB/4HY8
  • PDB/4I38
  • PDB/4I39
  • PDB/4I3A
  • PDB/4I3I
  • PDB/4I3J