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Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 Å resolution reveals the presence of a new PLA 2 ‐like protein with a novel cys 32–Cys 49 disulphide bridge with a bound sugar at the substrate‐binding site
Author(s) -
Jabeen Talat,
Singh Nagendra,
Singh Rajendra K.,
Jasti Jayasankar,
Sharma Sujata,
Kaur Punit,
Srinivasan Alagiri,
Singh Tej P.
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20708
Subject(s) - crystallography , chemistry , monomer , crystal structure , stereochemistry , tetragonal crystal system , zinc , organic chemistry , polymer
The crystal structure of the phospholipase A2 (PLA 2 ) heterodimer from Naja naja sagittifera reveals the presence of a new PLA 2 ‐like protein with eight disulphide bridges. The heterodimer is formed between a commonly observed group I PLA 2 having seven characteristic disulfide bonds and a novel PLA 2 ‐like protein (Cys–PLA 2 ) containing two extra cysteines at two highly conserved sites (positions 32 and 49) of structural and functional importantance. The crystals of the heterodimer belong to tetragonal space group P41212 with cell dimensions, a = b = 77.7 Å and c = 68.4 Å corresponding to a solvent content of 33%, which is one of the lowest values observed so far in the PLA 2 crystals. The structure has been solved with molecular replacement method and refined to a final R value of 21.6% [ R free = 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 PLA 2 ‐like monomer. A non‐protein high‐quality electron density was also observed at the substrate‐binding site in the PLA 2 ‐like protein that has been interpreted as N ‐acetylglucosamine. The overall tertiary folds of the two monomers are similar having all features of PLA 2 ‐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–PLA 2 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 PLA 2 s. The N ‐acetylglucosamine molecule is favorably placed in the substrate‐binding site of Cys–PLA 2 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 PLA 2 and PLA2‐like proteins. The formation of heterodimer seems to have been induced by zinc ion. Proteins 2006. © 2005 Wiley‐Liss, Inc.