4GXI

R283K DNA polymerase beta binary complex with a templating 8OG

Summary for 4GXI

• Entry DOI: 10.2210/pdb4gxi/pdb
• Related: 4GXJ 4GXK
• Descriptor: DNA polymerase beta, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... (6 entities in total)
• Functional Keywords: transferase, lyase/dna polymerase, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 47786.82

Authors

Freudenthal, B.D.,Beard, W.A.,Wilson, S.H. (deposition date: 2012-09-04, release date: 2013-01-16, Last modification date: 2023-09-13)

Primary citation

Freudenthal, B.D.,Beard, W.A.,Wilson, S.H.
DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.
Nucleic Acids Res., 41:1848-1858, 2013

PubMed Abstract: A major base lesion resulting from oxidative stress is 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxoG) that has ambiguous coding potential. Error-free DNA synthesis involves 8-oxoG adopting an anti-conformation to base pair with cytosine whereas mutagenic bypass involves 8-oxoG adopting a syn-conformation to base pair with adenine. Left unrepaired the syn-8-oxoG/dAMP base pair results in a G-C to T-A transversion. During base excision repair of this mispair, DNA polymerase (pol) β is confronted with gap filling opposite 8-oxoG. To determine how pol β discriminates between anti- and syn-8-oxoG, we introduced a point mutation (R283K) to alter insertion specificity. Kinetic studies demonstrate that this substitution results in an increased fidelity opposite 8-oxoG. Structural studies with R283K pol β show that the binary DNA complex has 8-oxoG in equilibrium between anti- and syn-forms. Ternary complexes with incoming dCTP resemble the wild-type enzyme, with templating anti-8-oxoG base pairing with incoming cytosine. In contrast to wild-type pol β, the ternary complex of the R283K mutant with an incoming dATP-analogue and templating 8-oxoG resembles a G-A mismatched structure with 8-oxoG adopting an anti-conformation. These results demonstrate that the incoming nucleotide is unable to induce a syn-8-oxoG conformation without minor groove DNA polymerase interactions that influence templating (anti-/syn-equilibrium) of 8-oxoG while modulating fidelity.

PubMed: 23267011
DOI: 10.1093/nar/gks1276

Experimental method

X-RAY DIFFRACTION (1.949 Å)