Fig. 4.

A proposed model of the photoconversion of the RcaE GAF domain. In the Pr photoproduct state, PCB adopts C5-Z,syn/C10-Z,syn/C15-E,syn conformation and four pyrrole nitrogen atoms (N_A through N_D) are protonated. The proton of the PCB is provided by clustered water molecules in the porous cavity (dashed blue area) and stabilized by the negatively charged carboxylate of E217. We designate the unique GAF domain structure as “leaky bucket,” in which the large S2-S3 loop (pink) and the core of the antiparallel β-sheet (green) form a bucket, whereas the hydrophobic L249 and F252 in the H4 (yellow) form a lid. In the Pg dark state, the D-ring adopts C15-Z,anti conformation (red) and N_B is deprotonated while the other N_A, N_C, and N_D atoms are protonated. An alternative model with C15-Z,syn (blue) conformation discussed in the main text is also shown. The exact position of E217 in the Pg dark state is unclear.