Sand box 211: Difference between revisions

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Celina Pinto, Michal Harel

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 <Structure load='1EXN' size='500' frame='true' align='right' caption='T5 5'exonuclease' scene='Insert optional scene name here' />
-T5 5'-exonuclease is a homodimer composed of two identical chains, <scene name='Sand_box_211/Vghjvjh/2'>chain a</scene> and <scene name='Sand_box_211/Vhj/1'>chain b</scene>. Both chains contain a hole, bound by a helical arch composed of two helices<scene name='Sand_box_211/Helice_alpha/1'>TextToBeDisplayed</scene> in which hydrophobic<scene name='Sand_box_211/Hydrophobe/1'>TextToBeDisplayed</scene> and positively charged residues<scene name='Sand_box_211/Residus_plus/2'>TextToBeDisplayed</scene><scene name='Sand_box_211/Residus_plus/3'>TextToBeDisplayed</scene> <scene name='Sand_box_211/Hydrophobe_et_plus/1'>TextToBeDisplayed</scene>are located. The helical arch is situated in front of the active site and only single-stranded DNA can pass through it. Since the enzyme is able to cleave double-stranded DNA, the helical arch may be able to change conformation in order to free the active site.
+T5 5'-exonuclease is a homodimer composed of two identical chains, <scene name='Sand_box_211/Vghjvjh/2'>chain a</scene> and <scene name='Sand_box_211/Vhj/1'>chain b</scene>. Both chains contain a hole, bound by a helical arch composed of two helices in which hydrophobic and positively charged residuesare located. The helical arch is situated in front of the active site and only single-stranded DNA can pass through it. Since the enzyme is able to cleave double-stranded DNA, the helical arch may be able to change conformation in order to free the active site.
 The active site possesses 8 conserved acidic residues (Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. Tyr82 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.
 Six residues (Arg33, Lys83, Arg172, Lys 196, Lys215, Arg216 and Lys241) near the active site permit binding to branched DNA.