In E. coli., DNA polymerase I (coded by polA) is involved in the repair of damaged DNA and, in a subsidiary role, in semiconservative replication.

TLS Online TPP Program

#Id: 5894

#Unit 3. Fundamental Processes

When a nucleotide binds, the fingers domain rotates 60° toward the palm, with the tops of the fingers moving by 30 Å. The thumb domain also rotates toward the palm by 8°. 

These changes are cyclical:

They are reversed when the nucleotide is incorporated into the DNA chain, which then translocates through the enzyme to recreate an empty site.

TLS Online TPP Program

#Id: 5895

#Unit 3. Fundamental Processes

The palm domain is composed of a b sheet and contains the primary elements of the catalytic site. In particular, this region of DNA polymerase binds two divalent metal ions.

TLS Online TPP Program

#Id: 5896

#Unit 3. Fundamental Processes

One metal ion reduces the affinity of the 3’-OH for its hydrogen. This generates a 3’O- that is primed for the nucleophilic attack of the a-phosphate of the incoming dNTP. 

TLS Online TPP Program

#Id: 5897

#Unit 3. Fundamental Processes

The second metal ion coordinates the negative charges of the b-phosphate and g phosphate of the dNTP and stabilizes the pyrophosphate produced by joining the primer and the incoming nucleotide.

TLS Online TPP Program

#Id: 5898

#Unit 3. Fundamental Processes

The average number of nucleotides added before a polymerase dissociates defines its processivity. Nucleotides added per unit time dissociates defines its polymerisation

The 3’->5’ exonuclease activity removes the mispaired nucleotide, and the polymerase begins again known as proofreading

TLS Online TPP Program

#Id: 5899

#Unit 3. Fundamental Processes