Favored reaction mechanism of calcium-dependent phospholipase A(2). Insights from density functional exploration.
The sn-2 acyl hydrolysis of phospholipids catalyzed by phospholipase A(2) (PLA(2)) was investigated at the density functional B3LYP level. The PLA(2) active site is represented by quantum-chemical models that are based on available X-ray crystal structures. The two still controversial catalytic triad and calcium-coordinated oxyanion reaction mechanisms were considered. Tetrahedral intermediate formation in the first mechanism and the cleavage of the C-O bond in the second one are the rate-determining steps. Both mechanisms, in the gas phase and in the protein-like environment, yielded potential energy profiles with low energy barriers and consequently the comparison did not indicate a clear preference for one or the other path. An alternative mechanism, based on some corrections to the previously suggested ones, provides for an optional pathway for the enzyme activity.
Leopoldini
Monica
M
Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MIUR, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy.
Russo
Nino
N
Toscano
Marirosa
M
D055162:Biocatalysis; D002118:Calcium / Q000737:chemistry*; D020134:Catalytic Domain; D006860:Hydrogen Bonding; D006868:Hydrolysis; D010741:Phospholipases A / Q000737:chemistry / Q000378:metabolism*; D010743:Phospholipids / Q000378:metabolism; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
D010743:Phospholipids; D012997:Solvents; D010741:Phospholipases A; D002118:Calcium