1y75

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spinqualitylabelsall models 1y75, resolution 2.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

A new form of catalytically inactive phospholipase A2 with an unusual disulphide bridge Cys 32- Cys 49 reveals recognition for N-acetylglucosmine

Overview

The crystal structure of the phospholipase A2 (PLA2) heterodimer from Naja, naja sagittifera reveals the presence of a new PLA2-like protein with, eight disulphide bridges. The heterodimer is formed between a commonly, observed group I PLA2 having seven characteristic disulfide bonds and a, novel PLA2-like protein (Cys-PLA2) containing two extra cysteines at two, highly conserved sites (positions 32 and 49) of structural and functional, importance. The crystals of the heterodimer belong to tetragonal space, group P41212 with cell dimensions, a = b = 77.7 A and c = 68.4 A, corresponding to a solvent content of 33%, which is one of the lowest, values observed so far in the PLA2 crystals. The structure has been solved, with molecular replacement method and refined to a final R value of 21.6%, [Rfree = 25.6%]. The electron density revealed the presence of cysteines, 32 and 49 that are covalently linked to give rise to an eighth disulphide, bridge in the PLA2-like monomer. A non-protein high-quality electron, density was also observed at the substrate-binding site in the PLA2-like, protein that has been interpreted as N-acetylglucosamine. The overall, tertiary folds of the two monomers are similar having all features of, PLA2-type folding. A zinc ion is detected at the interface of the, heterodimer with fivefold coordination while another zinc ion was found on, the surface of Cys-PLA2 with sixfold coordination. The conformations of, the calcium-binding loops of both monomers are significantly different, from each other as well as from those in other group I PLA2s. The, N-acetylglucosamine molecule is favorably placed in the substrate-binding, site of Cys-PLA2 and forms five hydrogen bonds and several van der Waals, interactions with protein atoms, thus indicating a strong affinity. It, also provides clue of the possible mechanism of sugar recognition by PLA2, and PLA2-like proteins. The formation of heterodimer seems to have been, induced by zinc ion.

About this Structure

1Y75 is a Protein complex structure of sequences from Naja sagittifera with NAG and ZN as ligands. Active as Phospholipase A(2), with EC number 3.1.1.4 Full crystallographic information is available from OCA.

Reference

Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 A resolution reveals the presence of a new PLA2-like protein with a novel cys 32-Cys 49 disulphide bridge with a bound sugar at the substrate-binding site., Jabeen T, Singh N, Singh RK, Jasti J, Sharma S, Kaur P, Srinivasan A, Singh TP, Proteins. 2006 Feb 1;62(2):329-37. PMID:16287060

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