1NK7: Guanine-Adenine Mismatch At The Polymerase Active Site

Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.
PDB ID: 1NK7Download
MMDB ID: 105320
PDB Deposition Date: 2003/1/2
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Source Organism:
Geobacillus stearothermophilus
Similar Structures:
Biological Unit for 1NK7: trimeric; determined by author
Molecular Components in 1NK7
Label Count Molecule
Protein (1 molecule)
DNA Polymerase I
Molecule annotation
Nucleotides(2 molecules)
DNA Primer Strand
Molecule annotation
DNA Template Strand
Molecule annotation
Chemicals (7 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB