5h12

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Crystal structure of Deep Vent DNA Polymerase

Structural highlights

5h12 is a 1 chain structure with sequence from Pyrococcus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.502Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPOL_PYRSD In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.[UniProtKB:P77933] Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the 'homing site' in gene that lack the intein (Probable). Intein splicing has been shown to occur via a branched intermediate that is resolved as the reaction proceeds; formation of the branched intermediate is reversible in response to pH shifts (PubMed:8269515).[1]

Publication Abstract from PubMed

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 A 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.

Crystal structure of Deep Vent DNA polymerase.,Hikida Y, Kimoto M, Hirao I, Yokoyama S Biochem Biophys Res Commun. 2017 Jan 29;483(1):52-57. doi:, 10.1016/j.bbrc.2017.01.007. Epub 2017 Jan 4. PMID:28063932[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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References

  1. ↑ Xu MQ, Southworth MW, Mersha FB, Hornstra LJ, Perler FB. In vitro protein splicing of purified precursor and the identification of a branched intermediate. Cell. 1993 Dec 31;75(7):1371-7. PMID:8269515 doi:10.1016/0092-8674(93)90623-x
  2. ↑ Hikida Y, Kimoto M, Hirao I, Yokoyama S. Crystal structure of Deep Vent DNA polymerase. Biochem Biophys Res Commun. 2017 Jan 29;483(1):52-57. doi:, 10.1016/j.bbrc.2017.01.007. Epub 2017 Jan 4. PMID:28063932 doi:http://dx.doi.org/10.1016/j.bbrc.2017.01.007

Contents


PDB ID 5h12

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