3KHR: Dpo4 Post-Extension Ternary Complex With The Correct C Opposite The 2- Aminofluorene-Guanine [af]g Lesion

Citation:
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.
PDB ID: 3KHRDownload
MMDB ID: 80138
PDB Deposition Date: 2009/10/30
Updated in MMDB: 2012/09
Experimental Method:
x-ray diffraction
Resolution: 2.01  Å
Source Organism:
Sulfolobus solfataricus P2
Similar Structures:
Biological Unit for 3KHR: trimeric; determined by author and by software (PISA)
Molecular Components in 3KHR
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase IV(Gene symbol: SSO_RS11880)
Molecule annotation
Nucleotides(2 molecules)
1
5'-d(*tp*tp*gp*gp*ap*tp*gp*gp*tp*ap*gp*cp*(ddg))-3'
Molecule annotation
1
5'-d(*cp*c*tp*ap*ap*cp*gp*cp*tp*ap*cp*cp*ap*tp*cp*cp*ap*ap* Cp*c)-3'
Molecule annotation
Chemicals (5 molecules)
1
1
2
3
3
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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