5H12

Crystal structure of Deep Vent DNA Polymerase

Summary for 5H12

• Entry DOI: 10.2210/pdb5h12/pdb
• Descriptor: Deep Vent DNA Polymerase (2 entities in total)
• Functional Keywords: dna polymerase, transferase
• Biological source: Pyrococcus
• Total number of polymer chains: 1
• Total formula weight: 90715.93

Authors

Hikida, Y.,Kimoto, M.,Hirao, I.,Yokoyama, S. (deposition date: 2016-10-07, release date: 2017-01-25, Last modification date: 2024-11-06)

Primary citation

Hikida, Y.,Kimoto, M.,Hirao, I.,Yokoyama, S.
Crystal structure of Deep Vent DNA polymerase.
Biochem. Biophys. Res. Commun., 483:52-57, 2017

PubMed Abstract: DNA polymerases are useful tools in various biochemical experiments. We have focused on the DNA polymerases involved in DNA replication including the unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px). Many reports have described the different combinations between unnatural base pairs and DNA polymerases. As an example, for the replication of the Ds-Px pair, Deep Vent DNA polymerase exhibits high efficiency and fidelity, but Taq DNA polymerase shows much lower efficiency and fidelity. In the present study, we determined the crystal structure of Deep Vent DNA polymerase in the apo form at 2.5 Å resolution. Using this structure, we constructed structural models of Deep Vent DNA polymerase complexes with DNA containing an unnatural or natural base in the replication position. The models revealed that the unnatural Ds base in the template-strand DNA clashes with the side-chain oxygen of Thr664 in Taq DNA polymerase, but not in Deep Vent DNA polymerase.

PubMed: 28063932
DOI: 10.1016/j.bbrc.2017.01.007

Experimental method

X-RAY DIFFRACTION (2.502 Å)