4BBV

The PB0 Photocycle Intermediate of Photoactive Yellow Protein

Summary for 4BBV

• Entry DOI: 10.2210/pdb4bbv/pdb
• Related: 1D7E 1F98 1F9I 1GSV 1GSW 1GSX 1KOU 1NWZ 1ODV 1OT6 1OT9 1OTA 1OTB 1OTD 1OTE 1OTI 1S1Y 1S1Z 1S4R 1S4S 1T18 1T19 1T1A 1T1B 1T1C 1TS0 1TS6 1TS7 1TS8 1UGU 1UWN 1UWP 1XFN 1XFQ 2D01 2D02 2PHY 2PYP 2PYR 3PHY 3PYP 4B9O 4BBT 4BBU
• Descriptor: PHOTOACTIVE YELLOW PROTEIN, 4'-HYDROXYCINNAMIC ACID (3 entities in total)
• Functional Keywords: photoreceptor, light sensor, chromophore, photoreceptor protein, receptor, sensory transduction, signaling protein, pas, lov
• Biological source: HALORHODOSPIRA HALOPHILA
• Total number of polymer chains: 1
• Total formula weight: 14052.73

Authors

Schotte, F.,Cho, H.S.,Kaila, V.R.I.,Kamikubo, H.,Dashdorj, N.,Henry, E.R.,Graber, T.J.,Henning, R.,Wulff, M.,Hummer, G.,Kataoka, M.,Anfinrud, P.A. (deposition date: 2012-09-28, release date: 2012-11-14, Last modification date: 2019-01-30)

Primary citation

Schotte, F.,Cho, H.S.,Kaila, V.R.I.,Kamikubo, H.,Dashdorj, N.,Henry, E.R.,Graber, T.J.,Henning, R.,Wulff, M.,Hummer, G.,Kataoka, M.,Anfinrud, P.A.
Watching a Signaling Protein Function in Real Time Via 100-Ps Time-Resolved Laue Crystallography.
Proc.Natl.Acad.Sci.USA, 109:19256-, 2012

PubMed Abstract: To understand how signaling proteins function, it is crucial to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required to characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, and have used this capability to track the reversible photocycle of photoactive yellow protein (PYP) following trans-to-cis photoisomerization of its p-coumaric acid (pCA) chromophore over 10 decades of time. The first of four major intermediates characterized in this study is highly contorted, with the pCA carbonyl rotated nearly 90° out of the plane of the phenolate. A hydrogen bond between the pCA carbonyl and the Cys69 backbone constrains the chromophore in this unusual twisted conformation. Density functional theory calculations confirm that this structure is chemically plausible and corresponds to a strained cis intermediate. This unique structure is short-lived (∼600 ps), has not been observed in prior cryocrystallography experiments, and is the progenitor of intermediates characterized in previous nanosecond time-resolved Laue crystallography studies. The structural transitions unveiled during the PYP photocycle include trans/cis isomerization, the breaking and making of hydrogen bonds, formation/relaxation of strain, and gated water penetration into the interior of the protein. This mechanistically detailed, near-atomic resolution description of the complete PYP photocycle provides a framework for understanding signal transduction in proteins, and for assessing and validating theoretical/computational approaches in protein biophysics.

PubMed: 23132943
DOI: 10.1073/PNAS.1210938109

Experimental method

X-RAY DIFFRACTION (1.6 Å)