An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM

Abstract

C-Phycoerythrin (PE) from Phormidium sp. A09DM has been crystallized using different conditions and its structure determined to atomic resolution (1.14 Å). In order for the pigment present, phycoerythrobilin (PEB), to function as an efficient light-harvesting molecule it must be held rigidly (Kupka and Scheer in Biochim Biophys Acta 1777:94–103, 2008) and, moreover, the different PEB molecules in PE must be arranged, relative to each other, so as to promote efficient energy transfer between them. This improved structure has allowed us to define in great detail the structure of the PEBs and their binding sites. These precise structural details will facilitate theoretical calculations of each PEB’s spectroscopic properties. It was possible, however, to suggest a model for which chromophores contribute to the different regions of absorption spectrum and propose a tentative scheme for energy transfer. We show that some subtle differences in one of these PEB binding sites in two of the 12 subunits are caused by crystal contacts between neighboring hexamers in the crystal lattice. This explains some of the differences seen in previous lower resolution structures determined at two different pH values (Kumar et al. in Photosyn Res 129:17–28, 2016).Electronic supplementary materialThe online version of this article (doi:10.1007/s11120-017-0443-2) contains supplementary material, which is available to authorized users.

Structure of Phycobilisomes

“…Three aromatic residues (phenylalanine or tyrosine) of the L R γ are located above ring D of the three β82 bilins, respectively, and induce geometrical changes in the D rings due to the strong π-π interactions. Moreover, an extra PEB from the L R γ has been found to be in close proximity to one of the three β82 bilins (named as the bilin-β 2 82 ), and the distance between them is within 3.0 Å. It is clear that the two specific bilins are strongly coupled, forming the delocalized electronic state with low energy.…”

“…It is clear that the two specific bilins are strongly coupled, forming the delocalized electronic state with low energy. Compared to the other two β82 bilins, the π-electron clouds of the bilin-β 2 82 are subjected to greater modulation and may therefore provide an important site of light harvesting and energy migration in the inner cavity of rods. A similar pathway was also observed in a R-PE crystal structure (50).…”

Dichromic Allophycocyanin Trimer Covering a Broad Spectral Range (550–660 nm)

“…The conformation of PEB was obtained from C‐phycoerythrin of the marine cyanobacterium Phormidium sp. A09DM [49] (pdb: 5NB3). The conformation of PΦB that was consulted from phytochrome B of Sorghum bicolor [50] (pdb: 6TC5) and followed the conformation of PCB in the APC structure from Mastigocladus laminosus .…”

The Unique Light-Harvesting System of the Algal Phycobilisome: Structure, Assembly Components, and Functions

“…Most PBPs covalently couple with phycobilins through the sulphydryl group of cysteine, generally forming a thioether bond with C31 of the A-ring of PBP. In some phycobiliproteins, C31 of the A-ring and C181 of the D-ring of phycocyanin can form two thioether bonds with two cysteine sulphydryl groups simultaneously [25]. In addition, there are PBP subunits, such as ApcE, that are coupled to PCB through non-covalent bonds [26].…”