DNA Polymerase I: Difference between revisions
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==Overview== | |||
DNA replication is catalyzed by '''DNA polymerase.''' All cells express several different DNA polymerases that variously participate in the several aspects of DNA replication and in the repair of damaged DNA. DNA polymerases catalyze the reaction (DNA)<sub>n residues</sub> + dNTP → (DNA)<sub>n+1 residues</sub> + PP<sub>''i''</sub>, where dNTP is the deoxynucleoside triphosphate whose base is complementary to a base on the strand being copied, the so-called '''template strand.''' In addition, DNA polymerases cannot initiate replication by linking together two dNTPs, but rather, can only link the incoming nucleotide to a terminal 3'-OH group on an existing polynucleotide strand, the so-called '''primer strand,''' thereby forming a 3' → 5' phosphodiester bond between successive deoxynucleotides. | DNA replication is catalyzed by '''DNA polymerase.''' All cells express several different DNA polymerases that variously participate in the several aspects of DNA replication and in the repair of damaged DNA. DNA polymerases catalyze the reaction (DNA)<sub>n residues</sub> + dNTP → (DNA)<sub>n+1 residues</sub> + PP<sub>''i''</sub>, where dNTP is the deoxynucleoside triphosphate whose base is complementary to a base on the strand being copied, the so-called '''template strand.''' In addition, DNA polymerases cannot initiate replication by linking together two dNTPs, but rather, can only link the incoming nucleotide to a terminal 3'-OH group on an existing polynucleotide strand, the so-called '''primer strand,''' thereby forming a 3' → 5' phosphodiester bond between successive deoxynucleotides. | ||
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These active sites occupy different regions of Pol I. In fact, mild treatment of Pol I by proteases such as trypsin and subtilisin, cleaves Pol I into two catalytically active fragments. The N-terminal fragment (residues 1-323) contains the 5' → 3' exonuclease function, whereas the larger, C-terminal fragment (residues 324-928), which is known as the '''Klenow fragment,''' contains both the polymerase and the 3' → 5' exonuclease functions. | These active sites occupy different regions of Pol I. In fact, mild treatment of Pol I by proteases such as trypsin and subtilisin, cleaves Pol I into two catalytically active fragments. The N-terminal fragment (residues 1-323) contains the 5' → 3' exonuclease function, whereas the larger, C-terminal fragment (residues 324-928), which is known as the '''Klenow fragment,''' contains both the polymerase and the 3' → 5' exonuclease functions. | ||
==Structure of the Klenow fragment== | |||
<applet load='1KLN_pymol.pdb' size='500' frame='true' align='right' caption='Klenow–DNA' scene='Sandbox_dvoet/DNA_polymerase/Klenow-dna/4' /> | <applet load='1KLN_pymol.pdb' size='500' frame='true' align='right' caption='Klenow–DNA' scene='Sandbox_dvoet/DNA_polymerase/Klenow-dna/4' /> | ||
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==Structure of ''E. coli'' DNA polymerase I== | |||
<applet load='1KLN_pymol.pdb' size='450' frame='true' align='right' caption='Klenow–DNA closeup' scene='Sandbox_dvoet/DNA_polymerase/Klenow-dna-closeup/4' /> | <applet load='1KLN_pymol.pdb' size='450' frame='true' align='right' caption='Klenow–DNA closeup' scene='Sandbox_dvoet/DNA_polymerase/Klenow-dna-closeup/4' /> | ||
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==Structure of Klentaq1 in its closed and open forms== | |||
<applet load='1taq.pdb' size='450' frame='true' align='right' caption='Thermus aquaticus Pol I' scene= 'Sandbox_dvoet/DNA_polymerase/Taq_pol_i/1'/> | <applet load='1taq.pdb' size='450' frame='true' align='right' caption='Thermus aquaticus Pol I' scene= 'Sandbox_dvoet/DNA_polymerase/Taq_pol_i/1'/> | ||
