Virtuelle (Nano) Welten: PDB Molecule of the Month 3: DNA Polymerase

Exploring the Structure

These simple DNA polymerases are shaped roughly like a hand. Both are from bacteria: on the left is the enzyme from Escherichia coli, PDB entry 1kln, and on the right is the enzyme from Thermus aquaticus, PDB entry 1tau. A cleaved version of the E. coli enzyme was studied: the missing part, which you will not find in the PDB file, is shown with a green outline. The space between the "fingers" and the "thumb" is just the right size for a DNA helix. But surprisingly, DNA actually fits into the palm when the enzyme is at work. In these pictures, the template strand is colored purple and the new strand is colored green. The enzyme contains three separate active sites. The polymerase site, near the top in these pictures, synthesizes the new strand by adding nucleotides. The 3'-5' exonuclease site, near the center in the E. coli polymerase, proofreads the new additions. The polymerase from Thermus aquaticus does not have this proofreading ability--perhaps the heat in which it lives performs the same function. At the bottom is the 5' exonuclease site that later removes the small RNA fragments that are used to prime DNA replication.
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