Diverse Roles of Glycine Residues Conserved in Photoactive Yellow Proteins

The role of glycine residues was studied by alanine-scanning mutagenesis using photoactive yellow protein, a structural prototype of PER ARNT SIM domain proteins, as a template. Mutation of glycine located close to the end of β-strands with dihedral angles disallowed for alanine (Gly-37, Gly-59, Gly-86, and Gly-115) induces destabilization of the protein structure. On the other hand, substitution for Gly-77 and Gly-82, incorporated into the fifth α-helix, slows the photocycle by 15–20 times, suggesting that these residues regulate the light-induced structural switch between dark-state structure and signaling-state structure. Most importantly, a significant amount of G29A is in the bleached state and showed a 1000-fold slower photocycle. As Oɛ2 of the carboxylic acid of Glu-46 is close enough for contact with Cα of Gly-29, alanine mutation perturbs this packing. Fourier transform infrared spectroscopy demonstrated that the COɛ2 stretching mode of Glu-46 is 6 cm−1 upshifted in G29A, suggesting that Cα of Gly-29 acts as a proton donor for the Cα-H…Oɛ2 hydrogen bond with Glu-46, which stabilizes the dark-state structure. During the photocycle, Glu-46 becomes negatively charged by donating a proton to the chromophore, resulting in breakage of this hydrophobic packing and consequent conformational change of the protein.