Sand box 211: Difference between revisions

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Lys196 is positioned between two metal sites. Its mutation perturbs metal ion binding. Lys215, Arg216 and Lys241 are important for binding to the 5' overhanging hairpin substrate. Furthermore, residues Lys215 and Arg216 form part of a helix–loop–helix feature. Arg33 binds to a phosphodiester residue in the 3' end of the cleavage site.

The reaction only takes place if at least two divalent metal ions are bound to the enzyme. However, the DNA binding doesn't need the presence of metal ions. Metal ions participate in the enzymatic catalysis of phosphodiester bond in several ways. For example, they can act as a nucleophile or a general base. They also participate in the catalysis of phosphate diester hydrolysis reactions by interacting with the oxygens which are not involved in the scissile phosphate.

[[Image:mg.jpg | thumb | left | The metal ions' interaction]]The reaction only takes place if at least two divalent metal ions are bound to the enzyme. However, the DNA binding doesn't need the presence of metal ions. Metal ions participate in the enzymatic catalysis of phosphodiester bond in several ways. For example, they can act as a nucleophile or a general base. They also participate in the catalysis of phosphate diester hydrolysis reactions by interacting with the oxygens which are not involved in the scissile phosphate (figure left).

~~[[Image:mg.jpg]]~~

Following divalent metal ions permit the reaction to take place : Mn2+, Mg2+, Co2+, Zn2+, Fe2+ and Cu2+. However, the reaction is the most efficient with Mn2+ and Mg2+ as cofactors. Furthermore, it has been shown that T5 5'-exonuclease is able to cleave double-stranded closed-circular plasmids with an Mn2+ cofactor although this enzyme normally is only able to cleave single-stranded 5' ends.

Sand box 211: Difference between revisions

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@@ Line 30: / Line 30: @@
 Lys196 is positioned between two metal sites. Its mutation perturbs metal ion binding. Lys215, Arg216 and Lys241 are important for binding to the 5' overhanging hairpin substrate. Furthermore, residues Lys215 and Arg216 form part of a helix–loop–helix feature. Arg33 binds to a phosphodiester residue in the 3'  end of the cleavage site.
-The reaction only takes place if at least two divalent metal ions are bound to the enzyme. However, the DNA binding doesn't need the presence of metal ions. Metal ions participate in the enzymatic catalysis of phosphodiester bond in several ways. For example, they can act as a nucleophile or a general base. They also participate in the catalysis of phosphate diester hydrolysis reactions by interacting with the oxygens which are not involved in the scissile phosphate.
+[[Image:mg.jpg | thumb | left | The metal ions' interaction]]The reaction only takes place if at least two divalent metal ions are bound to the enzyme. However, the DNA binding doesn't need the presence of metal ions. Metal ions participate in the enzymatic catalysis of phosphodiester bond in several ways. For example, they can act as a nucleophile or a general base. They also participate in the catalysis of phosphate diester hydrolysis reactions by interacting with the oxygens which are not involved in the scissile phosphate (figure left).
-[[Image:mg.jpg]]
 Following divalent metal ions permit the reaction to take place : Mn2+, Mg2+, Co2+, Zn2+, Fe2+ and Cu2+. However, the reaction is the most efficient with Mn2+ and Mg2+ as cofactors. Furthermore, it has been shown that T5 5'-exonuclease is able to cleave double-stranded closed-circular plasmids with an Mn2+ cofactor although this enzyme normally is only able to cleave single-stranded 5' ends.