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Contents 1 Background 2 Function 3 Structure 4 Sources

Background

The discovery of DNA Polymerase I is credited to Arthur Kornberg in 1955. Kornberg and his colleagues isolated RNA pol I from E. coli extracts through a DNA assay (Lehman). This enzyme was the first DNA polymerase discovered, and was therefore given the name DNA Polymerase I. Research has also shown that other forms of the protein can be isolated from other bacterium including Thermus aquaticus (Lawyer). This organism gave us taq polymerase, which is highly useful in polymerase chain reaction due to its polymerizing properties as well as its ability to withstand very high temperatures.

During prokaryotic replication, RNA nucleotide primers are laid down to provide a 3' hydroxyl for DNA polymerase III to elongate the replicated DNA strand. However, this primer must be removed and replaced with DNA nucleotides and bonded to the remaining strand. This role is carried out by DNA Polymerase I.

Function

In prokaryotic DNA replication, DNA Polymerase I is first called into action to remove the RNA primer laid down by DNA primase. DNA pol I will use its 5' to 3' exonuclease activity in order to excise RNA nucleotides from the replicated DNA strand. This is a unique ability in prokaryotic conditions, making primer removal the primary job of the enzyme.

Replacing the nucleotides is accomplished by the 5' to 3' polymerase activity of DNA polymerase I. This activity is how polymerases can add on deoxynucleoside triphosphates, dNTPs, on to an existing 3' hydroxyl and is shared between all DNA polymerases in E. coli. This activity along with its relatively slow processivity, only about 15 to 20 nucleotides per second compared to pol III at about 1000 nucleotides per second, makes DNA polymerase I perfect for its specific role (Camps). Primers on the replicated strands are only 10 base pairs long, so polymerase I has a very short sequence to remove and replace. Additionally, DNA Polymerase I also has 3' to 5' exonuclease activity, which is also shared between many polymerases (Pierce). This means that the enzyme is able to reverse direction and return back upstream of where it has already added on new nucleotides, and remove previous bases. This allows for the pol I to proofread and edit its own work, which is essential to fidelity of the replication process. Both the 5' to 3' polymerase and 3' to 5' exonuclease active sites are found in the Klenow Fragment (see Structure section).

One weakness in the function of DNA polymerase I, is that the enzyme is incapable of forming a phosphodiester bond between a 3' hydroxyl and pre-existing 5' phosphate group. Therefore, a helper enzyme known as ligase can come in and connect the DNA placed by pol I to the DNA placed by pol III all throughout replication. This finalizes the activity of DNA polymerase I and results in a full strand of repllcated DNA.

Structure

DNA Polymerase I is a hetero trimer comprised of six chains with three distinct sequences. Each of the sequences is repeated twice within the molecule ("COCRYSTAL"). Two of the six chains are polypeptide chains, each comprised of 580 amino acids. They have identical secondary structures consisting of 31 alpha helices and 20 beta pleated sheets. Another distinct sequence found in DNA Polymerase is a short polypeptide chain that is 9 amino acids in length. The final distinct sequence is a sequence that is 12 nucleotides in length. Each lengthy DNA chain has a condensed tertiary structure. A short polypeptide chain and a DNA chain burrow into the center of the condensed DNA strand, creating the quaternary structure of the molecule. The two condensed chains form a disulfide bond and form a parallel structure (RCSB).

DNA Polymerase I is composed of

spinqualitylabelsall models DNA Polymerase I Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

. The first domain is the N-terminus domain, found at the beginning of the polypeptide strand. This terminus is colored in blue. The second domain is the finger domain. This domain has the capability to change its configuration to open or close the conformation of the Polymerase. When Tyr 671, a residue in the finger domain, is base paired with a formation called template G, DNA Polymerase is in an open conformation. When Tyr 671 moves aside, the active site is exposed and the DNA Polymerase is in a closed conformation. The final domain is the C-terminus, in red, also known as the Klenow fragment (RCSB).

The molecule contains several ligands around its perimeter that aid in the binding of DNA to the enzyme. There are two DAD ligands which are dideoxyadenosine triphosphates. There are also five ligands, in black, which are simply zinc ions. There are two sucrose ligands referred to as residues, enlarged and in green. Finally, there are three sulfate ions, known as the ligands ("COCRYSTAL").

Sources

1. Camps, M., & Loeb, L. A. (2004). When pol I goes into high gear: processive DNA synthesis by pol I in the cell. Cell Cycle, 3(2), 114-116.

2. "COCRYSTAL STRUCTURE OF BACILLUS FRAGMENT DNA POLYMERASE I WITH DUPLEX DNA , DCTP, AND ZINC (CLOSED FORM)." OCA Browser-database for Structure/function. N.p., 8 Feb. 2006. Web. 10 Feb. 2017.

3. Lawyer, F. C., Stoffel, S., Saiki, R. K., Myambo, K., Drummond, R., & Gelfand, D. H. (1989). Isolation, characterization, and expression in Escherichia coli of the DNA polymerase gene from Thermus aquaticus. Journal of Biological Chemistry, 264(11), 6427-6437.

4. Lehman, I. R. (2003). Discovery of DNA polymerase. Journal of Biological Chemistry, 278(37), 34733-34738.

5. Pierce, B. A. (2012). Genetics: A conceptual approach. Macmillan.

6. RCSB Protein Data Bank, Golosov, A.A., Warren, J.J., Beese, L.S., Karplus, M. "3EZ5." RCSB PDB - 3EZ5: Cocrystal Structure of Bacillus Fragment DNA Polymerase I with Duplex DNA , DCTP, and Zinc (closed Form). Structure Summary Page. N.p., n.d. Web. 10 Feb. 2017.