Exploring the 3D Structure

 


On this page, you can see the structure of Thermus aquaticus DNA Polymerase. While it spins, notice the shape of the protein. It has several functional parts that are discussed below. After each button is pressed, you can explore the zoomed-in region by clicking and rotating.

Reset and spin the Taq DNA Polymerase. Alpha helices are colored pink and beta strands are colored yellow.

View the most highly conserved amino acid motifs among Taq DNA Polymerase and its orthologs. Motif A is in blue, motif B is in red and motif C is in yellow.

This is the polymerizing region of the Taq DNA Polymerase. It is shaped like an "open hand." Notice the finger region (blue), the thumb region (yellow), and the palm region (red). The finger region is responsible for recognition of the four deoxyribonucleotide bases. This domain rotates inward 46° to add nucleotides to the growing DNA strand.

Look at the active site of the polymerizing region. The active site amino acids Asp 610, Asp 785 and Glu 786 are shown in light pink.

Colored orange is the 3' to 5' exonuclease region of the Taq DNA Polymerase. Though this region is nonfunctional in Taq DNA Polymerase, this is the location of 3' to 5' exonuclease activity in its orthologs.

Colored light blue is the 5' to 3' exonuclease region of the Taq DNA Polymerase. This region is functional in Taq DNA Polymerase, and it an function independently, if removed from the rest of the protein by a protease.

Explore the cleft of the 5' to 3' exonuclease region. This cleft contains carboxylates that bind diavlent metal ions including Zn and Mn. A zinc ion is shown shown in the active site in yellow. The characteristic beta-sheets in this area are colored blue.

All of the reference information above can be found on the pages for my favorite protein and my favorite orthologs. Please feel free to contact me via the email address below.


Molecular Biology Homepage - Davidson College Homepage - My Homepage

Questions and comments can be directed to ststreb@davidson.edu