PDBsum entry 3khh

Transferase/DNA

PDB id: 3khh

Contents

Protein chains

341 a.a.

DNA/RNA

Ligands

DGT ×2

_AF ×2

Metals

_CA ×6

Waters ×92

References listed in PDB file

Key reference

• Title: Mechanism of error-Free and semitargeted mutagenic bypass of an aromatic amine lesion by y-Family polymerase dpo4.
• Authors: O.Rechkoblit, A.Kolbanovskiy, L.Malinina, N.E.Geacintov, S.Broyde, D.J.Patel.
• Ref.: Nat Struct Biol, 2010, 17, 379-388.
• PubMed id: 20154704

Abstract

The aromatic amine carcinogen 2-aminofluorene (AF) forms covalent adducts with DNA, predominantly with guanine at the C8 position. Such lesions are bypassed by Y-family polymerases such as Dpo4 via error-free and error-prone mechanisms. We show that Dpo4 catalyzes elongation from a correct 3'-terminal cytosine opposite [AF]G in a nonrepetitive template sequence with low efficiency. This extension leads to cognate full-length product, as well as mis-elongated products containing base mutations and deletions. Crystal structures of the Dpo4 ternary complex, with the 3'-terminal primer cytosine base opposite [AF]G in the anti conformation and with the AF moiety positioned in the major groove, reveal both accurate and misalignment-mediated mutagenic extension pathways. The mutagenic template-primer-dNTP arrangement is promoted by interactions between the polymerase and the bulky lesion rather than by a base pair-stabilized misaligment. Further extension leads to semitargeted mutations via this proposed polymerase-guided mechanism.