1NKB: A Bacillus Dna Polymerase I Product Complex Bound To A Guanine-Thymine Mismatch After Three Rounds Of Primer Extension, Following Incorporation Of Dctp, Dgtp, And Dttp

Citation:
Abstract
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: 1NKBDownload
MMDB ID: 104397
PDB Deposition Date: 2003/1/2
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 1NKB: trimeric; determined by author
Molecular Components in 1NKB
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase I
Molecule annotation
Nucleotides(2 molecules)
1
DNA Primer Strand
Molecule annotation
1
DNA Template Strand
Molecule annotation
Chemicals (6 molecules)
1
2
2
3
3
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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