5DQH: Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Ethylthymidine

DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O(4)-Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4-O(4) bond on processing by human DNA polymerase eta (hPol eta) was studied for oligonucleotides containing O(4)-methylthymidine, O(4)-ethylthymidine, and analogs restricting the O(4)-methylene group in an anti-orientation. Primer extension assays revealed that the O(4)-alkyl orientation influences hPol eta bypass. Crystal structures of hPol eta*DNA*dNTP ternary complexes with O(4)-methyl- or O(4)-ethylthymidine in the template strand showed the nucleobase of the former lodged near the ceiling of the active site, with the syn-O(4)-methyl group engaged in extensive hydrophobic interactions. This unique arrangement for O(4)-methylthymidine with hPol eta, inaccessible for the other analogs due to steric/conformational restriction, is consistent with differences observed for nucleotide incorporation and supports the concept that lesion conformation influences extension across DNA damage. Together, these results provide mechanistic insights on the mutagenicity of O(4)MedT and O(4)EtdT when acted upon by hPol eta.
PDB ID: 5DQHDownload
MMDB ID: 142088
PDB Deposition Date: 2015/9/14
Updated in MMDB: 2016/08
Experimental Method:
x-ray diffraction
Resolution: 1.99  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 5DQH: trimeric; determined by author and by software (PISA)
Molecular Components in 5DQH
Label Count Molecule
Protein (1 molecule)
DNA Polymerase ETA(Gene symbol: POLH)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*cp*ap*tp*(5ej)p*ap*tp*gp*ap*cp*gp*cp*t)-3')
Molecule annotation
DNA (5'-d(*ap*gp*cp*gp*tp*cp*ap*t)-3')
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB