6W2M

Abortive ternary complex crystal structure of DNA polymerase Beta with 8OG-dC base pair at the primer terminus and flipped out dA

Summary for 6W2M

• Entry DOI: 10.2210/pdb6w2m/pdb
• Descriptor: DNA polymerase beta, Template Strand, Primer Strand, ... (9 entities in total)
• Functional Keywords: dna polymerase beta, conformational change, enzyme mechanism, transferase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 48667.75

Authors

Batra, V.K.,Wilson, S.H. (deposition date: 2020-03-06, release date: 2020-07-22, Last modification date: 2023-10-18)

Primary citation

Batra, V.K.,Wilson, S.H.
Structure of a DNA polymerase abortive complex with the 8OG:dA base pair at the primer terminus.
Commun Biol, 3:348-348, 2020

PubMed Abstract: Adenine frequently pairs with the Hoogsteen edge of an oxidized guanine base (8OG) causing G to T transversions. The (syn)8OG:dA base pair is indistinguishable from the cognant base pair and can be extended by DNA polymerases with reduced efficiency. To examine the structural basis of this reduced efficiency, we sought to obtain the structure of the "product" complex of DNA polymerase (pol) β with the (syn)8OG:dA base pair at the primer terminus by soaking the binary complex crystals with a hydrolysable dCTP analogue complementary to the template base G. Crystallographic refinement of the structure revealed that the adenine of the (syn)8OG:dA base pair had been expelled from the primer terminus and a dCMP was inserted opposite 8OG in a reverse orientation; another uninserted molecule of the analogue was bound to the templating base G. This leads to an abortive complex that could form the basis of oxidatively-induced pol β stalling.

PubMed: 32620932
DOI: 10.1038/s42003-020-1080-4

Experimental method

X-RAY DIFFRACTION (1.998 Å)