Fig. 7
From: Structural snapshot of a bacterial phytochrome in its functional intermediate state
Structural comparison of various phytochromes in different states of the photocycle. Proteins in ribbon representations, bilin chromophores in ball/stick representations. Selected conserved amino acids are highlighted as sticks, water molecules are shown as red spheres. In the Pfr state of bathy bacteriophytochromes (a, wild-type Agp2-PCM and b, Agp2-PAiRFP2; c, PaBphP-PCM (P. aeruginosa; PDB entry 3NHQ29)) Tyr165, Phe192 and Arg202 show a conserved conformation. Furthermore, the cysteines are always β-facially bound to BV. In the Meta-F state of Agp2-PAiRFP2, the two monomers (Mol A and B) of the asymmetric unit (d, e) show slightly different structures. In Mol A, the N-terminus including Cys13 is free of intermolecular interactions (Fig. 5). After illumination, Mol A reveals the BV isomerization and Cys13 in α-facially bound position accompanied by a conformational shift of the N-terminus and a conformational change of Phe192, Tyr165 and Arg202, together with the formation of a hydrogen bond bridge mediated by two water molecules (d, Wat722 and Wat732) between Tyr165 and Arg202. In Mol B (e), the N-terminus is tightly packed to Mol A (Fig. 5). In the Pr states of prototypical bacterial (f, Agp1-PCMSER13 of A. fabrum, PDB entry 5HSQ30 and g, DrBphP-PCM of D. radiodurans; e.g. PDB entry 4Q0J18), cyanobacterial (h, Cph1-PCM of Synchocystis sp.; PDB entry 2VEA31) and plant (i, AtPhyB-PCM of A. thaliana; PDB entry 4OUR32) phytochromes, the rotameric states of the corresponding amino acids as well as the same two water molecules between the Tyr and Arg residues are similar to Mol A in the Meta-F state of Agp2-PAiRFP2 (d). Because of the low resolution (3.4 Å), these water molecules were not resolved in the AtPhyB-PCM structure32
