Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

3KHH

Dpo4 extension ternary complex with a C base opposite the 2-aminofluorene-guanine [AF]G lesion

Summary for 3KHH
Entry DOI10.2210/pdb3khh/pdb
Related3KHG 3KHL 3KHR
DescriptorDNA polymerase IV, 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3', 5'-D(*CP*CP*TP*A*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3', ... (7 entities in total)
Functional Keywordslesion 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 sourceSulfolobus solfataricus P2
More
Cellular locationCytoplasm (Probable): Q97W02
Total number of polymer chains6
Total formula weight98958.75
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 citationRechkoblit, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.7 Å)
Structure validation

238895

PDB entries from 2025-07-16

PDB statisticsPDBj update infoContact PDBjnumon