A structural pathway for signaling in the E46Q mutant of photoactive yellow protein

Structure. 2005 Jan;13(1):55-63. doi: 10.1016/j.str.2004.10.016.


In the bacterial photoreceptor photoactive yellow protein (PYP), absorption of blue light by its chromophore leads to a conformational change in the protein associated with differential signaling activity, as it executes a reversible photocycle. Time-resolved Laue crystallography allows structural snapshots (as short as 150 ps) of high crystallographic resolution (approximately 1.6 A) to be taken of a protein as it functions. Here, we analyze by singular value decomposition a comprehensive time-resolved crystallographic data set of the E46Q mutant of PYP throughout the photocycle spanning 10 ns-100 ms. We identify and refine the structures of five distinct intermediates and provide a plausible chemical kinetic mechanism for their inter conversion. A clear structural progression is visible in these intermediates, in which a signal generated at the chromophore propagates through a distinct structural pathway of conserved residues and results in structural changes near the N terminus, over 20 A distant from the chromophore.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Crystallography, X-Ray
  • Databases as Topic
  • Hydrogen Bonding
  • Kinetics
  • Microspectrophotometry
  • Mutation*
  • Photoreceptors, Microbial / chemistry*
  • Photoreceptors, Microbial / genetics*
  • Photoreceptors, Microbial / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Signal Transduction*


  • Bacterial Proteins
  • Photoreceptors, Microbial

Associated data

  • PDB/1T18
  • PDB/1T19
  • PDB/1T1A
  • PDB/1T1B
  • PDB/1T1C
  • PDB/IE1
  • PDB/IE2
  • PDB/IL1
  • PDB/IL2
  • PDB/IL3