Stereochemistry of cleavage of internucleotide bonds by Serratia marcescens endonuclease

Endonuclease from Serratia marcescens hydrolyzes internucleotide phosphorothioate linkages of R P configuration with inversion of configuration at P-atom. This observation supports a reported architecture of the active site, with 3′-bridging and pro-S P non-bridging oxygen atoms of the scissile phosphate group involved in direct contact with hydrated magnesium cation, while His-89 activates a water molecule which attacks the phosphorus atom according to a one-step in-line mechanism. The presence of a phosphorothioate bond of S P configuration downstream to that one being cleaved reduces the rate of hydrolysis. This suggests participation of the pro-S P oxygen atom of that phosphate bond in the mechanism of action of the enzyme, which was not detected in published crystallographic analyses. Endonuclease from Serratia marcescens hydrolyzes internucleotide phosphorothioate linkages of R P configuration with inversion of configuration at P-atom.