Sand box 211: Difference between revisions

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The core regions of the enzyme are composed of beta-sheets and alpha-helices . 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/1'>acidic residues</scene> (Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. <scene name='Sand_box_211/Try82/1'>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.

The active site possesses 8 conserved <scene name='Sand_box_211/8_residus/3'>acidic residues</scene>(Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. <scene name='Sand_box_211/Try82/1'>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/1'>Six residues</scene> (Arg33, Lys83, Arg172, Lys 196, Lys215, Arg216 and Lys241) near the active site permit binding to branched DNA.

<scene name='Sand_box_211/Lys83/1'>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.

Sand box 211: Difference between revisions

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 The core regions of the enzyme are composed of beta-sheets and alpha-helices . 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/1'>acidic residues</scene> (Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. <scene name='Sand_box_211/Try82/1'>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.
+The active site possesses 8 conserved <scene name='Sand_box_211/8_residus/3'>acidic residues</scene>(Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. <scene name='Sand_box_211/Try82/1'>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/1'>Six residues</scene> (Arg33, Lys83, Arg172, Lys 196, Lys215, Arg216 and Lys241) near the active site permit binding to branched DNA.
 <scene name='Sand_box_211/Lys83/1'>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.