3UMD

Structure of pB intermediate of Photoactive yellow protein (PYP) at pH 4.

Summary for 3UMD

• Entry DOI: 10.2210/pdb3umd/pdb
• Related: 3UME
• Descriptor: Photoactive yellow protein, 4'-HYDROXYCINNAMIC ACID (3 entities in total)
• Functional Keywords: photoreceptor, signal transduction, protein binding
• Biological source: Halorhodospira halophila
• Total number of polymer chains: 1
• Total formula weight: 14052.73

Authors

Tripathi, S.,Srajer, V.,Purwar, N.,Henning, R.,Schmidt, M. (deposition date: 2011-11-13, release date: 2012-04-11, Last modification date: 2023-09-13)

Primary citation

Tripathi, S.,Srajer, V.,Purwar, N.,Henning, R.,Schmidt, M.
pH Dependence of the Photoactive Yellow Protein Photocycle Investigated by Time-Resolved Crystallography.
Biophys.J., 102:325-332, 2012

PubMed Abstract: Visualizing the three-dimensional structures of a protein during its biological activity is key to understanding its mechanism. In general, protein structure and function are pH-dependent. Changing the pH provides new insights into the mechanisms that are involved in protein activity. Photoactive yellow protein (PYP) is a signaling protein that serves as an ideal model for time-dependent studies on light-activated proteins. Its photocycle is studied extensively under different pH conditions. However, the structures of the intermediates remain unknown until time-resolved crystallography is employed. With the newest beamline developments, a comprehensive time series of Laue data can now be collected from a single protein crystal. This allows us to vary the pH. Here we present the first structure, to our knowledge, of a short-lived protein-inhibitor complex formed in the pB state of the PYP photocycle at pH 4. A water molecule that is transiently stabilized in the chromophore active site prevents the relaxation of the chromophore back to the trans configuration. As a result, the dark-state recovery is slowed down dramatically. At pH 9, PYP stops cycling through the pB state altogether. The electrostatic environment in the chromophore-binding site is the likely reason for this altered kinetics at different pH values.

PubMed: 22339869
DOI: 10.1016/j.bpj.2011.11.4021

Experimental method

X-RAY DIFFRACTION (1.8 Å)