6FBG

KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fifth primer nucleotide.

Summary for 6FBG

• Entry DOI: 10.2210/pdb6fbg/pdb
• Descriptor: DNA polymerase I, thermostable, DNA (5'-D(*GP*AP*CP*CP*AP*CP*AP*(OH3)P*CP*GP*GP*C)-3'), DNA (5'-D(*AP*AP*AP*CP*GP*CP*CP*GP*GP*TP*GP*TP*GP*GP*TP*C)-3'), ... (7 entities in total)
• Functional Keywords: dna polymerase, modified nucleotides, klentaq, klentaq dna polymerase, dna binding protein
• Biological source: Thermus aquaticus; More
• Total number of polymer chains: 3
• Total formula weight: 70737.35

Authors

Kropp, H.M.,Diederichs, K.,Marx, A. (deposition date: 2017-12-19, release date: 2018-09-26, Last modification date: 2024-05-08)

Primary citation

Kropp, H.M.,Durr, S.L.,Peter, C.,Diederichs, K.,Marx, A.
Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.
Proc. Natl. Acad. Sci. U.S.A., 115:9992-9997, 2018

PubMed Abstract: DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification "moves" from the 3'-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme's activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.

PubMed: 30224478
DOI: 10.1073/pnas.1811518115

Experimental method

X-RAY DIFFRACTION (1.702 Å)