SNAP output for PDB entry 5dlg [SNAP web server]

PDB-id

5dlg; SNAP-derived features in text and JSON formats; DNAproDB

Class

transferase-DNA

Method

X-ray (2.351 Å)

Summary

Crystal structure of human DNA polymerase eta inserting dgmpnpp opposite o4-methylhymidine

Reference

O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ (2016): "Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta." Chem Sci, 7, 4896-4904. doi: 10.1039/C6SC00666C.

Abstract

DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O₄-Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4-O₄ bond on processing by human DNA polymerase η (hPol η) was studied for oligonucleotides containing O₄-methylthymidine, O₄-ethylthymidine, and analogs restricting the O₄-methylene group in an anti-orientation. Primer extension assays revealed that the O₄-alkyl orientation influences hPol η bypass. Crystal structures of hPol η•DNA•dNTP ternary complexes with O₄-methyl- or O₄-ethylthymidine in the template strand showed the nucleobase of the former lodged near the ceiling of the active site, with the syn-O₄-methyl group engaged in extensive hydrophobic interactions. This unique arrangement for O₄-methylthymidine with hPol η, 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 O₄MedT and O₄EtdT when acted upon by hPol η.