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The Mechanism of Phosphorylation of Natural Nucleosides and Anti‐HIV Analogues by Nucleoside Diphosphate Kinase Is Independent of Their Sugar Substituents
Author(s) -
Hutter Michael C.,
Helms Volkhard
Publication year - 2002
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/1439-7633(20020703)3:7<643::aid-cbic643>3.0.co;2-l
Subject(s) - chemistry , nucleoside diphosphate kinase , residue (chemistry) , stereochemistry , ribose , nucleoside , adenosine diphosphate , cytidine , enzyme , phosphorylation , kinase , nucleoside triphosphate , nucleotide , biochemistry , platelet , platelet aggregation , gene , immunology , biology
Abstract The reaction mechanism of the phosphoryl transfer catalyzed by dinucleoside diphosphate kinase from Dictyostelium discoideum is investigated by semiempirical AM1 molecular orbital computation of an active site model system on the basis of various X‐ray crystallographic structures. The computational results suggest that the phosphoryl transfer from adenosine triphosphate to the His122 residue is accompanied by the simultaneous shift of a proton from the histidine residue to one of the oxygen atoms of the γ phosphate group. This involves a doubly protonated His122 residue whilst this residue is neutral in its ternary complex with ADP and the transition state analogue AlF 3 . The proposed mechanism is thus analogous to that of phosphoryl transfer by cyclic adenosine monophosphate dependent protein kinase and uridine/cytidine monophosphate kinase as found in our earlier work and clarifies the role of the ribose 3′‐OH group. Furthermore, the energetics of phosphoryl transfer onto other nucleoside analogues such as 3′‐azido‐3′‐deoxythymidine‐diphosphate and 2′,3′‐dideoxy‐2′,3′‐didehydro‐thymidine‐diphosphate are investigated. The calculated reaction barriers for the phosphorylation of the diphosphates by the enzyme are all within a range of 13.1 kJ mol −1 , which suggests that variations in the activation energies alone cannot account for the experimentally observed differences in enzymatic activity. Consequences for the design of new anti‐HIV nucleoside analogues are discussed.