4RQ2

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MnCl2 for 35 s

Summary for 4RQ2

• Entry DOI: 10.2210/pdb4rq2/pdb
• Related: 4RPX 4RPY 4RPZ 4RQ0 4RQ1 4RQ3 4RQ4 4RQ5 4RQ6 4RQ7 4RQ8
• Descriptor: DNA polymerase beta, DNA (5'-D(P*GP*TP*CP*GP*G)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'), ... (9 entities in total)
• Functional Keywords: x-family, pol beta, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P06746
• Total number of polymer chains: 4
• Total formula weight: 49875.83

Authors

Vyas, R.,Reed, A.J.,Suo, Z. (deposition date: 2014-10-31, release date: 2015-04-15, Last modification date: 2023-09-20)

Primary citation

Vyas, R.,Reed, A.J.,Tokarsky, E.J.,Suo, Z.
Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.
J.Am.Chem.Soc., 137:5225-5230, 2015

PubMed Abstract: One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg(2+) appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.

PubMed: 25825995
DOI: 10.1021/jacs.5b02109

Experimental method

X-RAY DIFFRACTION (2.2 Å)