Sand box 211: Difference between revisions
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<scene name='Sand_box_211/Lys83/2'>Lys83</scene> is positioned in the helical arch region close to metal site 1. It has an important binding role as well as a catalytic role. It was shown that DNA binding is pH dependent which means that the T5 5'-exonuclease requires protonation of Lys83 to be able to bind to DNA. The mechanism of the Lys83 in the catalytic activity is still unknown, but it has been proposed that Lys83 acts as a general base/acid activating water to attack the scissile phosphodiester bond and protonating the leaving oxygen. | <scene name='Sand_box_211/Lys83/2'>Lys83</scene> is positioned in the helical arch region close to metal site 1. It has an important binding role as well as a catalytic role. It was shown that DNA binding is pH dependent which means that the T5 5'-exonuclease requires protonation of Lys83 to be able to bind to DNA. The mechanism of the Lys83 in the catalytic activity is still unknown, but it has been proposed that Lys83 acts as a general base/acid activating water to attack the scissile phosphodiester bond and protonating the leaving oxygen. | ||
<scene name='Sand_box_211/Lys196/2'>Lys196</scene> is positioned between two metal sites. Its mutation perturbs metal ion binding. | <scene name='Sand_box_211/Lys196/2'>Lys196</scene> is positioned between two metal sites. Its mutation perturbs metal ion binding. | ||
<scene name='Sand_box_211/Lys215arg216lys241/2'>Lys215, Arg216 and Lys241</scene> 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. | <scene name='Sand_box_211/Lys215arg216lys241/2'>Lys215, Arg216 and Lys241</scene> are important for binding to the 5' overhanging hairpin substrate. Furthermore, residues | ||
<scene name='Sand_box_211/Lys215216/2'>Lys215 and Arg216</scene> form part of a helix–loop–helix feature. <scene name='Sand_box_211/Arg33/1'>Arg33</scene> binds to a phosphodiester residue in the 3' end of the cleavage site. | |||
[[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 | 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). | ||