Structural and sequence analyses of an unusual bacteriophytochrome from R. palustris

Abstract

Bacteriophytochromes (Bphs) are bacterial red‐light photoreceptors found in photosynthetic and non‐photosynthetic bacteria. Bphs undergo reversible photoconversion between two distinct red (Pr) and far‐red (Pfr) light absorbing states. An organic cofactor, biliverdin (BV) is required for Pr/Pfr photoconversion. Bphs are composed of a photosensory core (PC) including PAS, GAF and PHY domains and an effector domain, usually a histidine kinase. We report on the preliminary crystal structure of the unusual Bph from Rhodopseudomonas palustris, RpBphP3 (P3) PC bound to BV in the Pr state. Unlike classical Bphs, P3 photoconverts between Pr and near‐red (Pnr) states. P3 crystals (30–60 □m in all dimensions) yielded diffraction at 100 K to a maximum resolution of 2.8 Å. P3 crystals are in P212121 space group with unit cell dimensions of a=155.92 Å, b=185.32 Å, and c=199.53 Å. The initial P3 structure was determined with the molecular replacement (MR) method implemented in HKL3000 using the crystal structure of P3 lacking PHY domain (PDB ID code 2OOL) as search model. P3 crystallized as a dimer, which is physiologically relevant oligomeric state of the protein. Informed by structural and sequence analyses, we identify amino acids in the BV‐binding pocket of P3 and at the dimer interface that play a role in the unusual photochemistry and fluorescence of this protein.