5UGO

DNA polymerase beta nick complex with imidodiphosphate

Summary for 5UGO

• Entry DOI: 10.2210/pdb5ugo/pdb
• Related: 5UGN 5UGP
• Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... (7 entities in total)
• Functional Keywords: transferase, lyase, dna domain, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 48254.19

Authors

Freudenthal, B.D.,Wilson, S.H.,Beard, W.A. (deposition date: 2017-01-09, release date: 2017-07-26, Last modification date: 2024-03-06)

Primary citation

Shock, D.D.,Freudenthal, B.D.,Beard, W.A.,Wilson, S.H.
Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction.
Nat. Chem. Biol., 13:1074-1080, 2017

PubMed Abstract: DNA polymerases catalyze efficient and high-fidelity DNA synthesis. While this reaction favors nucleotide incorporation, polymerases also catalyze a reverse reaction, pyrophosphorolysis, that removes the DNA primer terminus and generates deoxynucleoside triphosphates. Because pyrophosphorolysis can influence polymerase fidelity and sensitivity to chain-terminating nucleosides, we analyzed pyrophosphorolysis with human DNA polymerase β and found the reaction to be inefficient. The lack of a thio-elemental effect indicated that this reaction was limited by a nonchemical step. Use of a pyrophosphate analog, in which the bridging oxygen is replaced with an imido group (PNP), increased the rate of the reverse reaction and displayed a large thio-elemental effect, indicating that chemistry was now rate determining. Time-lapse crystallography with PNP captured structures consistent with a chemical equilibrium favoring the reverse reaction. These results highlight the importance of the bridging atom between the β- and γ-phosphates of the incoming nucleotide in reaction chemistry, enzyme conformational changes, and overall reaction equilibrium.

PubMed: 28759020
DOI: 10.1038/nchembio.2450

Experimental method

X-RAY DIFFRACTION (1.897 Å)