3KHL

Dpo4 post-extension ternary complex with misinserted A opposite the 2-aminofluorene-guanine [AF]G lesion

Summary for 3KHL

• Entry DOI: 10.2210/pdb3khl/pdb
• Related: 3KHG 3KHH 3KHR
• Descriptor: DNA polymerase IV, 5'-D(*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*AP*(DDG))-3', 5'-D(*CP*C*TP*AP*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3', ... (7 entities in total)
• Functional Keywords: lesion bypass, dna polymerase, y-family polymerase, 2-aminofluorene, semi-targeted mutagenesis, dna damage, dna repair, dna replication, dna-binding, dna-directed dna polymerase, magnesium, metal-binding, mutator protein, nucleotidyltransferase, transferase, transferase-dna complex, transferase/dna
• Biological source: Sulfolobus solfataricus P2; More
• Cellular location: Cytoplasm (Probable): Q97W02
• Total number of polymer chains: 6
• Total formula weight: 99535.14

Authors

Rechkoblit, O.,Malinina, L.,Patel, D.J. (deposition date: 2009-10-30, release date: 2010-02-16, Last modification date: 2023-09-06)

Primary citation

Rechkoblit, O.,Kolbanovskiy, A.,Malinina, L.,Geacintov, N.E.,Broyde, S.,Patel, D.J.
Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.
Nat.Struct.Mol.Biol., 17:379-388, 2010

PubMed 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.

PubMed: 20154704
DOI: 10.1038/nsmb.1771

Experimental method

X-RAY DIFFRACTION (2.1 Å)