4RNM: Crystal structure of human polymerase eta inserting dAMPnPP opposite DNA template containing an abasic site

The most common lesion in DNA is an abasic site resulting from glycolytic cleavage of a base. In a number of cellular studies, abasic sites preferentially code for dATP insertion (the "A rule"). In some cases frameshifts are also common. X-ray structures with abasic sites in oligonucleotides have been reported for several microbial and human DNA polymerases (pols), e.g. Dpo4, RB69, KlenTaq, yeast pol iota, human (h) pol iota, and human pol beta. We reported previously that hpol eta is a major pol involved in abasic site bypass (Choi, J.-Y., Lim, S., Kim, E. J., Jo, A., and Guengerich, F. P. (2010 J. Mol. Biol. 404, 34-44). hpol eta inserted all four dNTPs in steady-state and pre-steady-state assays, preferentially inserting A and G. In LC-MS analysis of primer-template pairs, A and G were inserted but little C or T was inserted. Frameshifts were observed when an appropriate pyrimidine was positioned 5' to the abasic site in the template. In x-ray structures of hpol eta with a non-hydrolyzable analog of dATP or dGTP opposite an abasic site, H-bonding was observed between the phosphate 5' to the abasic site and water H-bonded to N1 and N6 of A and N1 and O6 of G nucleoside triphosphate analogs, offering an explanation for what appears to be a "purine rule." A structure was also obtained for an A inserted and bonded in the primer opposite the abasic site, but it did not pair with a 5' T in the template. We conclude that hpol eta, a major copying enzyme with abasic sites, follows a purine rule, which can also lead to frameshifts. The phenomenon can be explained with H-bonds.
PDB ID: 4RNMDownload
MMDB ID: 127119
PDB Deposition Date: 2014/10/24
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 2.144  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 4RNM: trimeric; determined by author
Molecular Components in 4RNM
Label Count Molecule
Protein (1 molecule)
DNA Polymerase ETA(Gene symbol: POLH)
Molecule annotation
Nucleotides(2 molecules)
DNA Template: Cat(3dr)atgacgct
Molecule annotation
DNA Primar: Agcgtcat
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

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