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structure of dna polymerase i klenow fragment science klenow fragment of escherichia coli dna polymerase i which was cocrystallized with duplex dna positioned 11 base pairs of dna in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3 to 5 exonuclease domain dna polymerase i the other three domains work to her to sustain dna polymerase activity e coli bacteria contains 5 different dna polymerases dna pol i dna pol ii dna pol iii dna pol iv and dna pol v eukaryotic cells contain 5 different dna polymerases α β γ δ and ε dna polymerase i an overview dna polymerase i dna polymerase i is a single polypeptide chain with 928 amino acids and molecular weight of 109 kda it has three sites which provide three distinct catalytic activities 3′ to 5′ exonuclease 5′ to 3′ exonuclease and 5′ to 3′ polymerase dna polymerase since dna polymerase requires a free 3 oh group for initiation of synthesis it can synthesize in only one direction by extending the 3 end of the preexisting nucleotide chain hence dna polymerase moves along the template strand in a 3 –5 direction and the daughter strand is formed in a 5 –3 direction the structure of dna polymerase i klenow fragment bound to the structure of dna polymerase i klenow fragment bound to duplex dna background klenow fragment of dna pol i by sundeep kang dna pol i consists of a single dna polymerase i proteopedia life in 3d parison of these two structures reveals that the structure on the left the so called closed conformation differs from the that on the right the so called open conformation by a hinge like motion of the fingers domain away from the polymerase active site the rest of the protein remains very nearly unchanged bacterial dna polymerase i joyce cm potapova o delucia am et al 2008 fingers‐closing and other rapid conformational changes in dna polymerase i klenow fragment and their role in nucleotide selectivity biochemistry 47 6103–6116 rothwell pj and waksman g 2005 structure and mechanism of dna polymerases advances in protein chemistry 71 401–440 dna polymerases structural diversity and mon mechanisms figure 1 a parison of primer template dna bound to four dna polymerases the plexes shown in a b and d are co crystal structures whereas the plex in c is anatomy of a polymerase how structure effects function neb accurate genome replication is critical for the viability of an organism the general concept for copying dna was evident upon the elucidation of dna’s double
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