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From Proteopedia

Revision as of 06:15, 15 February 2017

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. SOURCE This enzyme was the first DNA polymerase discovered, and was therefore given the name DNA Polymerase I. It plays a key role in prokaryotic DNA replication.

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

DNA Polymerase I has the ability to manipulate DNA in three separate ways. It is similar to DNA Polymerase III, as it has 5' to 3' polymerase activity to elongate the replicated DNA strand along with 3' to 5' exonuclease activity for proofreading and editing the new DNA. Both of the active sites for these functions are found in the Klenow Fragment. Clip thing

Its primary role is removing the RNA primers initially laid down by the RNA polymerase primase and replacing those nucleotides with dNTPs. The initial step of excising RNA nucleotides on the replicated strand is made possible due to its 5' to 3' exonuclease activity. The enzyme will remove then add on DNA nucleotides 5' to 3' and connect these nucleotides by phosphodiester bonds.

Its function is parallel to the eukaryotic DNA polymerase BLANK.

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. 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.

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.

Sources

"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.

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

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.