DNA Polymerase I: Difference between revisions
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<applet load='1KLN_pymol.pdb' size=' | <applet load='1KLN_pymol.pdb' size='450' frame='true' align='right' caption='Klenow–DNA closeup' scene='Sandbox_dvoet/DNA_polymerase/Klenow-dna-closeup/4' /> | ||
The X-ray structure is that of an editing complex, that is, the 3' end of the primer strand, the end that is elongated by the polymerase, occupies the 3'→5' exonuclease active site. This is more clearly seen in a <scene name='Sandbox_dvoet/DNA_polymerase/Klenow-dna-closeup/3'>closeup of the DNA</scene> in which the the rods connecting successive P atoms have been removed for clarity. Note that the base pair closest to the polymerase active site, a G·C, has opened up to enable the 3' end of the primer strand to reach the exonuclease active site. Click here to <scene name='Sandbox_dvoet/DNA_polymerase/Dna-closeup/3'>hide the protein</scene>. | The X-ray structure is that of an editing complex, that is, the 3' end of the primer strand, the end that is elongated by the polymerase, occupies the 3'→5' exonuclease active site. This is more clearly seen in a <scene name='Sandbox_dvoet/DNA_polymerase/Klenow-dna-closeup/3'>closeup of the DNA</scene> in which the the rods connecting successive P atoms have been removed for clarity. Note that the base pair closest to the polymerase active site, a G·C, has opened up to enable the 3' end of the primer strand to reach the exonuclease active site. Click here to <scene name='Sandbox_dvoet/DNA_polymerase/Dna-closeup/3'>hide the protein</scene>. | ||
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<applet load='1taq.pdb' size=' | <applet load='1taq.pdb' size='450' frame='true' align='right' caption='Thermus aquaticus Pol I' scene= 'Sandbox_dvoet/DNA_polymerase/Taq_pol_i/1'/> | ||
As mentioned above, Pol I's primary and essential function is to excise the RNA primers from newly synthesized Okazaki fragments with its 5' → 3' exonuclease function and replace them with DNA using its polymerase function. This yields a double-stranded DNA (dsDNA) with a single strand nick between successive Okazaki fragments, a nick that is eventually sealed through the action of DNA ligase. | As mentioned above, Pol I's primary and essential function is to excise the RNA primers from newly synthesized Okazaki fragments with its 5' → 3' exonuclease function and replace them with DNA using its polymerase function. This yields a double-stranded DNA (dsDNA) with a single strand nick between successive Okazaki fragments, a nick that is eventually sealed through the action of DNA ligase. | ||
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<applet load='3ktq.pdb' size=' | <applet load='3ktq.pdb' size='450' frame='true' align='left' caption='Klentaq1–Closed conformation' scene= 'Sandbox_dvoet/DNA_polymerase/Klentaq1-ddctp/2'/> | ||
<applet load='2ktq.pdb' size=' | <applet load='2ktq.pdb' size='450' frame='true' align='right' caption='Klentaq1–Open conformation' scene= 'Sandbox_dvoet/DNA_polymerase/Klentaq1-open_conformation/2'/> | ||
Here, Klentaq1's N-terminal, palm, fingers and thumb domains are yellow, magenta, green, and blue, respectively. The DNA is drawn in stick form colored according to atom type (template C cyan, primer C green, N blue, O red, and P orange). | Here, Klentaq1's N-terminal, palm, fingers and thumb domains are yellow, magenta, green, and blue, respectively. The DNA is drawn in stick form colored according to atom type (template C cyan, primer C green, N blue, O red, and P orange). | ||
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<applet load='3ktq.pdb' size=' | <applet load='3ktq.pdb' size='450' frame='true' align='left' caption='Klentaq1–Closed closeup' scene= 'Sandbox_dvoet/DNA_polymerase/Klentaq1-closed_closeup/3'/> | ||
<applet load='2ktq.pdb' size=' | <applet load='2ktq.pdb' size='450' frame='true' align='right' caption='Klentaq1–Open closeup' scene= 'Sandbox_dvoet/DNA_polymerase/Klentaq1-open_closeup/6'/> | ||
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). | ||
