Structural Analysis of Phospholipase A₂ from Functional Perspective. 1. Functionally Relevant Solution Structure and Roles of the Hydrogen-Bonding Network^†,‡

Bovine pancreatic phospholipase A₂ (PLA2), a small (13.8 kDa) Ca²⁺-dependent lipolytic enzyme, is rich in functional and structural character. In an effort to examine its detailed structure−function relationship, we determined its solution structure by multidimensional nuclear magnetic resonance (NMR) spectroscopy at a functionally relevant pH. An ensemble of 20 structures generated has an average root-mean-square deviation (RMSD) of 0.62 ± 0.08 Å for backbone (N, C^α, C) atoms and 0.98 ± 0.09 Å for all heavy atoms. The overall structure shows several notable differences from the crystal structure:  the first three residues at the N-terminus, the calcium-binding loop (Y25−T36), and the surface loop (V63−N72) appear to be flexible; the α-helical conformation of helix B (E17−F22) is absent; helix D appears to be shorter (D59−V63 instead of D59−D66); and the hydrogen-bonding network is less defined. These differences were analyzed in relation to the function of PLA2. We then further examined the H-bonding network, because its functional role or even its existence in solution has been in dispute recently. Our results show that part of the H-bonding network (the portion away from N-terminus) clearly exists in solution, as evidenced by direct observation (at 11.1 ppm) of a strong H-bond between Y73 and D99 and an implicated interaction between D99 and H48. Analyses of a series of mutants indicated that the existence of the Y73···D99 H-bond correlates directly with the conformational stability of the mutant. Loss of this H-bond results in a loss of 2−3 kcal/mol in the conformational stability of PLA2. The unequivocal identification and demonstration of the structural importance of a specific hydrogen bond, and the magnitude of its contribution to conformational stability, are uncommon to the best of our knowledge. Our results also suggest that, while the D99···H48 catalytic diad is the key catalytic machinery of PLA2, it also helps to maintain conformational integrity.