4O3S

Crystal structure of human polymerase eta extending an 8-oxog dna lesion: post insertion of 8-oxog-dc pair

Summary for 4O3S

• Entry DOI: 10.2210/pdb4o3s/pdb
• Related: 4O3N 4O3O 4O3P 4O3Q 4O3R
• Descriptor: DNA polymerase eta, DNA (5'-D(*CP*AP*TP*GP*(8OG)P*TP*GP*AP*CP*GP*CP*T)-3'), DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*C)-3'), ... (7 entities in total)
• Functional Keywords: catalytic domain, dna, dna damage, dna-directed dna polymerase, cytosine triphosphate, y-family polymerase, trans-lesion synthesis (tls), dna binding, 8-oxog lesion bypass, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: Q9Y253
• Total number of polymer chains: 3
• Total formula weight: 55038.28

Authors

Patra, A.,Egli, M. (deposition date: 2013-12-18, release date: 2014-04-30, Last modification date: 2023-09-20)

Primary citation

Patra, A.,Nagy, L.D.,Zhang, Q.,Su, Y.,Muller, L.,Guengerich, F.P.,Egli, M.
Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta
J.Biol.Chem., 289:16867-16882, 2014

PubMed Abstract: DNA damage incurred by a multitude of endogenous and exogenous factors constitutes an inevitable challenge for the replication machinery. Cells rely on various mechanisms to either remove lesions or bypass them in a more or less error-prone fashion. The latter pathway involves the Y-family polymerases that catalyze trans-lesion synthesis across sites of damaged DNA. 7,8-Dihydro-8-oxo-2'-deoxyguanosine (8-oxoG) is a major lesion that is a consequence of oxidative stress and is associated with cancer, aging, hepatitis, and infertility. We have used steady-state and transient-state kinetics in conjunction with mass spectrometry to analyze in vitro bypass of 8-oxoG by human DNA polymerase η (hpol η). Unlike the high fidelity polymerases that show preferential insertion of A opposite 8-oxoG, hpol η is capable of bypassing 8-oxoG in a mostly error-free fashion, thus preventing GC→AT transversion mutations. Crystal structures of ternary hpol η-DNA complexes and incoming dCTP, dATP, or dGTP opposite 8-oxoG reveal that an arginine from the finger domain assumes a key role in avoiding formation of the nascent 8-oxoG:A pair. That hpol η discriminates against dATP exclusively at the insertion stage is confirmed by structures of ternary complexes that allow visualization of the extension step. These structures with G:dCTP following either 8-oxoG:C or 8-oxoG:A pairs exhibit virtually identical active site conformations. Our combined data provide a detailed understanding of hpol η bypass of the most common oxidative DNA lesion.

PubMed: 24759104
DOI: 10.1074/jbc.M114.551820

Experimental method

X-RAY DIFFRACTION (1.717 Å)