4O3N: Crystal Structure Of Human Dna Polymerase Eta In Ternary Complex With Native Dna And Incoming Nucleotide (dcp)

Citation:
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 eta (hpol eta). Unlike the high fidelity polymerases that show preferential insertion of A opposite 8-oxoG, hpol eta is capable of bypassing 8-oxoG in a mostly error-free fashion, thus preventing GC-->AT transversion mutations. Crystal structures of ternary hpol eta-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 eta 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 eta bypass of the most common oxidative DNA lesion.
PDB ID: 4O3NDownload
MMDB ID: 119768
PDB Deposition Date: 2013/12/18
Updated in MMDB: 2014/07
Experimental Method:
x-ray diffraction
Resolution: 1.58  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4O3N: trimeric; determined by author and by software (PISA)
Molecular Components in 4O3N
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase ETA(Gene symbol: POLH)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*cp*ap*tp*gp*ap*tp*gp*ap*cp*gp*cp*t)-3')
Molecule annotation
1
DNA (5'-d(*ap*gp*cp*gp*tp*cp*ap*t)-3')
Molecule annotation
Chemicals (4 molecules)
1
1
2
2
3
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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