TAQ polymerase (DNA synthesizer)/DNA complex
Thermus aquaticus (bacteria)
DNA polymerases are responsible for duplicating deoxyribonucleic acid (DNA). They have two functions: editing double-stranded DNA that needs fixing and polymerizing, that is extending, DNA. The polymerase chain reaction, which is a standard technique nowadays to duplicate DNA from existing templates, makes use of a polymerase. A piece of DNA that should be duplicated is separated into its two strands by heat and to each strand a short complementary DNA strand, the primer, is attached. Polymerase is then used to complete each strand starting at the primer site. As each cycle creates two copies of the original DNA, just a limited number of cycles is capable of creating a large amount of what was initially just one DNA molecule. The reaction involves heat to denature the DNA and thus would seem difficult to automate since it would like also denature the polymerase used in the experiment. The solution comes from archaea that can live in extreme environments. An archaea, Thermus aquaticus, produces a polymerase that can function under these conditions. This polymerase is called taq polymerase and is used in commercial DNA synthesizers.
The structure here shows that protein. One can clearly see two very distinct and spatially separate domains. The smaller domain, carrying a zinc ion, is an exonuclease domain. The large domain, shaped almost like a hand or a baseball glove, holds a piece of DNA. The DNA sits in a deep , U-shaped cleft formed by two portions of the polymerase domain. These are called, because the overall shape so obviously resembles a hand holding DNA, the palm and the thumb domain. Comparison with other known polymerase structures shows that they all bind DNA in a similar fashion.
Protein Data Bank (PDB)
Eom, S.H. Wang, J. Steitz, T.A.; "Structure of Taq ploymerase with DNA at the polymerase active site."; Nature; (1996) 382:278-281 PubMed:8717047.
author: Arno Paehler