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.
Koziołkiewicz
M
M
Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lódź, Poland.
Owczarek
A
A
Domañski
K
K
Nowak
M
M
Guga
P
P
Stec
W J
WJ
D002384:Catalysis; D020134:Catalytic Domain; D004720:Endonucleases / Q000737:chemistry / Q000378:metabolism*; D006868:Hydrolysis; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D012706:Serratia marcescens / Q000201:enzymology*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013237:Stereoisomerism; D013873:Thionucleotides / Q000737:chemistry / Q000378:metabolism*
D009838:Oligodeoxyribonucleotides; D013873:Thionucleotides; D004720:Endonucleases; D008274:Magnesium