Journal of Biological Chemistry
Volume 291, Issue 39, September 2016, Pages 20674-20691
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Protein Structure and Folding
The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers*

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Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion.

conformational change
crystal structure
histidine kinase
photoreceptor
signal transduction
tertiary structure
Agrobacterium
phytochrome
quaternary structure

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The atomic coordinates and structure factors (codes 5HSQ and 5I5L) have been deposited in the Protein Data Bank (http://wwpdb.org/).

*

This work was supported by Deutsche Forschungsgemeinschaft Research Grants SFB498-B2 (to T. L. and N. K.) and SFB1078-B6 (to P. S.), Cluster of Excellence “Unifying Concepts in Catalysis” Research Field D3/E3-1 (to P. S.), a Queen Mary University of London Postgraduate Research Studentship (to S. N.), and by University of London Central Research Fund AR/CRF/B (to S. N.). The authors declare that they have no conflict of interest with the contents of this article.

1

Both authors contributed equally to this work.

2

Present address: Justus-Liebig-Universität Giessen, Institut für Pflanzenphysiologie, Senckenbergstr. 3, D-35390 Giessen, Germany.