DNA Polymerase I: Difference between revisions
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<applet load='3ktq.pdb' size='450' frame='true' align='left' caption='Klentaq1–Closed conformation ([[3ktq]])' scene= 'Sandbox_dvoet/DNA_polymerase/Klentaq1-ddctp/2'/> | <applet load='3ktq.pdb' size='450' frame='true' align='left' caption='Klentaq1–Closed conformation ([[3ktq]])' scene= 'Sandbox_dvoet/DNA_polymerase/Klentaq1-ddctp/2' name='Closed' /> | ||
<applet load='2ktq.pdb' size='450' frame='true' align='right' caption='Klentaq1–Open conformation ([[2ktq]])' scene= 'Sandbox_dvoet/DNA_polymerase/Klentaq1-open_conformation/2'/> | <applet load='2ktq.pdb' size='450' frame='true' align='right' caption='Klentaq1–Open conformation ([[2ktq]])' scene= 'Sandbox_dvoet/DNA_polymerase/Klentaq1-open_conformation/2' name='Open' /> | ||
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This, together with other experimental measurements, indicates that Klentaq1 rapidly samples the available dNTPs in its open conformation, but only when it binds the correct dNTP in a Watson–Crick pairing with the template base does it form the catalytically competent closed conformation. In addition, note how the template G that base pairs with the ddCTP in the closed conformation, moves away from the active site in the open conformation, in which it has no base pairing partner. | This, together with other experimental measurements, indicates that Klentaq1 rapidly samples the available dNTPs in its open conformation, but only when it binds the correct dNTP in a Watson–Crick pairing with the template base does it form the catalytically competent closed conformation. In addition, note how the template G that base pairs with the ddCTP in the closed conformation, moves away from the active site in the open conformation, in which it has no base pairing partner. | ||
<scene name='Sandbox_dvoet/DNA_polymerase/Klentaq1-closed_closeup/3' target='Closed' >closed closeup</scene> | |||
<scene name='Sandbox_dvoet/DNA_polymerase/Klentaq1-open_closeup/6' target='Open' >open closeup</scene> | |||
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A closeup of the active site region in the open conformation (''right'') reveals that the side chain of the conserved Tyr 671 (colored with C pink) is stacked on top of the template G that forms a base pair with the bound ddCTP, where it apparently participates in verifying that a Watson–Crick base pair has formed. In the closed conformation (''left''), Tyr 671, which is part of the fingers domain, has moved aside, presumably to permit the active site to form about the incoming dNTP (satisfy yourself that the Tyr 671 side chain is stacked on the template G in the open form but not in the closed form). | A closeup of the active site region in the open conformation (''right'') reveals that the side chain of the conserved Tyr 671 (colored with C pink) is stacked on top of the template G that forms a base pair with the bound ddCTP, where it apparently participates in verifying that a Watson–Crick base pair has formed. In the closed conformation (''left''), Tyr 671, which is part of the fingers domain, has moved aside, presumably to permit the active site to form about the incoming dNTP (satisfy yourself that the Tyr 671 side chain is stacked on the template G in the open form but not in the closed form). | ||