Crystal structure analysis of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM

Abstract

The role of unique sequence features of C-phycoerythrin, isolated from Phormidium sp. A09DM, has been investigated by crystallographic studies. Two conserved indels (i.e. inserts or deletions) are found in the β-subunit of Phormidium phycoerythrin that are distinctive characteristics of large number of cyanobacterial sequences. The identified signatures are a two-residue deletion from position 21 and a nine-residue insertion at position 146. Crystals of Phormidium phycoerythrin were obtained at pH values of 5 and 8.5, and structures have been resolved to high precision at 1.95 and 2.1 Å resolution, respectively. In both the structures, heterodimers of α- and β- subunits assemble as hexamers. The 7-residue insertion at position 146 significantly reduces solvent exposure of π-conjugated A-C rings of a phycoerythrobilin (PEB) chromophore, and can influence energy absorption and energy transfer characteristics. The structural analyses (with 12-fold redundancy) suggest that protein micro-environment alone dictates the conformation of bound chromophores. The low- and high-energy absorbing chromophores are identified based on A-B ring coplanarity. The spatial distribution of these is found to be similar to that observed in R-phycoerythrin, suggesting the direction of energy transfer from outer-surface of hexamer to inner-hollow cavity in the Phormidium protein. The crystal structures also reveal that a commonly observed Hydrogen-bonding network in phycobiliproteins, involving chromophore bound to α-subunit and amino acid at position 73 of β-subunit, may not be essential for structural and functional integrity of C-phycoerythrin orthologs. In solution, the protein displays slight red shift and decrease in fluorescence emission at acidic pH. The mechanism for which may be static and correlates with the proximity of +ve electric field of Arg148 to the C-ring of a PEB chromophore.

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

“…The symmetry of data and of the pH 7.5 crystals was found to be P 1 as was the symmetry of the pH 5 and 8.5 crystals obtained before (Kumar et al 2016 ). Similarly, the unit cell dimensions of all crystals are almost identical with no bigger difference than 1.7%.…”

“…The PE was isolated and purified from marine cyanobacteria Phormidium sp. A09DM as described earlier (Sonani et al 2015 ; Kumar et al 2016 ).…”

“…These monomer units then oligomerise to form trimers [(αβ) 3 ] and then stacked hexamers {[(αβ) 3 ] 2 }. The structure of this complex was first determined at two different pH values of 5 and 8.5 to the resolutions of 1.93 and 2.12 Å, respectively (PDB IDs: 5fvb and 5aqd, respectively; Kumar et al 2016 ). Since then we have been able to significantly improve the quality of the crystals of this pigment–protein complex and have determined its structure to atomic resolution of 1.14 Å.…”

“…The present report will describe the overall PEB binding pockets in more detail than was previously discussed for the cyanobacterial PE from Phormidium sp. A09DM (Kumar et al 2016 ). This earlier study also described subtle differences in the two crystal structures related to crystals being grown at different pHs, pH 5 and pH 8.5, respectively.…”

Phycoerythrin averts intracellular ROS generation and physiological functional decline in eukaryotes under oxidative stress

“…All six hydrophobic patches can express their antioxidant virtues in separated α-and β-subunits. Besides the apoprotein portion, the Phormidium PE contains two and three linear tetrapyrrol chromophors (called PEB) with their α-and β-subunits, respectively Kumar et al 2016). These phycoerythrobilins having plenty of conjugated pi-double bonds are efficient electron exchanger, which is the prerequisite to be an efficient antioxidant.…”