Ribonuclease H (RNase H) selectively degrades the RNA strand of RNA.DNA hybrids in a divalent cation-dependent manner. Previous structural studies revealed a single Mg(2+) ion-binding site in Escherichia coli RNase HI. In the crystal structure of the related RNase H domain of human immunodeficiency virus reverse transcriptase, however, two Mn(2+) ions were observed suggesting a different mode o...

Here, we used stopped-flow fluorescence techniques to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Effects of monovalent (K(+)) and divalent (Mg(2+), Mn(2+), Ca(2+), Zn(2+), Cu(2+), and Ni(2+)) metal ions on DNA binding and catalytic stages we...

The catalytic activity of phosphoenolpyruvate carboxykinase in rat liver cytosol is stimulated by incubating with Fe2+, Mn2+, Co2+, and Cd2+. When purified, the enzyme no longer responds to Fe2+, Co2+, or Cd2+ but retains a response to Mn2+. Low concentrations of SO4(2-) in the incubation medium with enzyme and divalent transition metal allow stimulation by Fe2+ and Co2+ and enhance the respons...

In vitro selection was used to isolate five classes of allosteric hammerhead ribozymes that are triggered by binding to certain divalent metal ion effectors. Each of these ribozyme classes are similarly activated by Mn2+, Fe2+, Co2+, Ni2+, Zn2+ and Cd2+, but their allosteric binding sites reject other divalent metals such as Mg2+, Ca2+ and Sr2+. Through a more comprehensive survey of cations, i...

A mechanism is proposed for the RNA-catalyzed reactions involved in RNA splicing and RNase P hydrolysis of precursor tRNA. The mechanism postulates that chemical catalysis is facilitated by two divalent metal ions 3.9 A apart, as in phosphoryl transfer reactions catalyzed by protein enzymes, such as the 3',5'-exonuclease of Escherichia coli DNA polymerase I. One metal ion activates the attackin...

The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the phosphate group located 3' to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the...

Various kinds of roles of the water molecules in the electronic states of the complexes of metal ions (M ) and deoxyribonucleic acid (DNA) are reviewed. Divalent metal ions M like Fe, Mn, Zn and so on, form Metal-DNA complexes (M -DNA) with each metal ion between the bases of a base pair of DNA. The electronic states of the complexes depend on the species of ions in M -DNA. Metal ions in Fe-DNA...