1S4S

Reaction Intermediate in the Photocycle of PYP, intermediate occupied between 100 micro-seconds to 5 milli-seconds

Summary for 1S4S

• Entry DOI: 10.2210/pdb1s4s/pdb
• Related: 1S4R
• Descriptor: Photoactive yellow protein, 4'-HYDROXYCINNAMIC ACID (3 entities in total)
• Functional Keywords: reaction intermediate, photosynthesis
• Biological source: Halorhodospira halophila
• Total number of polymer chains: 1
• Total formula weight: 14052.73

Authors

Schmidt, M.,Pahl, R.,Srajer, V.,Anderson, S.,Ren, Z.,Ihee, H.,Rajagopal, S.,Moffat, K. (deposition date: 2004-01-17, release date: 2004-04-13, Last modification date: 2023-10-25)

Primary citation

Schmidt, M.,Pahl, R.,Srajer, V.,Anderson, S.,Ren, Z.,Ihee, H.,Rajagopal, S.,Moffat, K.
Protein kinetics: Structures of intermediates and reaction mechanism from time-resolved x-ray data
Proc.Natl.Acad.Sci.USA, 101:4799-4804, 2004

PubMed Abstract: We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of time-dependent difference electron density maps spanning the time range from 5 micros to 100 ms. The successful fit of exponentials to right singular vectors derived from a singular value decomposition of the difference maps demonstrates that a chemical kinetic mechanism holds and that structurally distinct intermediates exist. We identify two time-independent difference maps, from which we refine the structures of the corresponding intermediates. We thus demonstrate how structures associated with intermediate states can be extracted from the experimental, time-dependent crystallographic data. Stoichiometric and structural constraints allow the exclusion of one kinetic mechanism proposed for the photocycle but retain other plausible candidate kinetic mechanisms.

PubMed: 15041745
DOI: 10.1073/pnas.0305983101

Experimental method

X-RAY DIFFRACTION (1.9 Å)