Sand box 211: Difference between revisions
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<scene name='Sand_box_211/Sheet/1'>beta-sheets</scene>. These form the base of the active site pocket which bind the catalytic metal ions. | <scene name='Sand_box_211/Sheet/1'>beta-sheets</scene>. These form the base of the active site pocket which bind the catalytic metal ions. | ||
The active site possesses 8 conserved <scene name='Sand_box_211/8_residus/ | The active site possesses 8 conserved <scene name='Sand_box_211/8_residus/4'>acidic residues</scene> (Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. <scene name='Sand_box_211/Try82/2'>Tyr82</scene> is also a conserved residue located in the active site, but it doesn't seem to have an important role since its mutation doesn't dramatically change the affinity to bind DNA. | ||
<scene name='Sand_box_211/6residus/ | <scene name='Sand_box_211/6residus/3'>Six residues</scene> (Arg33, Lys83, Arg172, Lys196, Lys215, Arg216 and Lys241) near the active site permit binding to branched DNA. | ||
<scene name='Sand_box_211/Lys83/ | <scene name='Sand_box_211/Lys83/3'>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 | <scene name='Sand_box_211/Lys215arg216lys241/2'>Lys215, Arg216 and Lys241</scene> are important for binding to the 5' overhanging hairpin substrate. Furthermore, residues | ||