Stereochemistry of cleavage of internucleotide bonds by Serratia marcescens endonuclease Original Research Article

Endonuclease from Serratia marcescens hydrolyzes internucleotide phosphorothioate linkages of RP configuration with inversion of configuration at P-atom. This observation supports a reported architecture of the active site, with 3′-bridging and pro-SP 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 SP configuration downstream to that one being cleaved reduces the rate of hydrolysis. This suggests participation of the pro-SP oxygen atom of that phosphate bond in the mechanism of action of the enzyme, which was not detected in published crystallographic analyses.