S. Sundell et al., A PROPOSAL FOR THE CATALYTIC MECHANISM IN PHOSPHOLIPASE-C BASED ON INTERACTION ENERGY AND DISTANCE GEOMETRY CALCULATIONS, Protein engineering, 7(4), 1994, pp. 571-577
The non-specific phospholipase C from Bacillus cereus preferentially h
ydrolyses phosphatidylcholine but is also active against phosphatidyls
erine, phosphatidylethanolamine and at a much lower level, sphingomyel
in. A minimal substrate model containing all required structural and c
onfigurational elements of a high affinity substrate was docked into t
he active site. The enzyme-substrate attachment points were from molec
ular interaction energy calculations using the program GRID and from a
previous phosphate inhibitor complex structure. Available conformatio
nal space for the substrate was sampled by distance geometry calculati
ons using the program DGEOM. This investigation clearly identifies the
attacking nucleophile, a catalytically favourable orientation of the
phosphate group in its tetra-, as well as its penta-, coordinated stat
e and a crucial stabilizing environment for the alkoxide intermediate.
Based on this information a complete catalytic cycle is proposed.