3PNC

Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer terminus and sodium at catalytic metal site

Summary for 3PNC

• Entry DOI: 10.2210/pdb3pnc/pdb
• Related: 3PML 3PMN
• Descriptor: DNA polymerase lambda, 5'-D(*CP*AP*GP*TP*AP*G)-3', 5'-D(*CP*GP*GP*CP*CP*TP*TP*AP*CP*TP*G)-3', ... (9 entities in total)
• Functional Keywords: protein-dna complex, lyase, transferase, dna, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: Q9UGP5
• Total number of polymer chains: 4
• Total formula weight: 43806.90

Authors

Bebenek, K.,Pedersen, L.C.,Kunkel, T.A. (deposition date: 2010-11-18, release date: 2011-02-02, Last modification date: 2024-02-21)

Primary citation

Bebenek, K.,Pedersen, L.C.,Kunkel, T.A.
Replication infidelity via a mismatch with Watson-Crick geometry.
Proc.Natl.Acad.Sci.USA, 108:1862-1867, 2011

PubMed Abstract: In describing the DNA double helix, Watson and Crick suggested that "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." Indeed, among many mispairing possibilities, either tautomerization or ionization of bases might allow a DNA polymerase to insert a mismatch with correct Watson-Crick geometry. However, despite substantial progress in understanding the structural basis of error prevention during polymerization, no DNA polymerase has yet been shown to form a natural base-base mismatch with Watson-Crick-like geometry. Here we provide such evidence, in the form of a crystal structure of a human DNA polymerase λ variant poised to misinsert dGTP opposite a template T. All atoms needed for catalysis are present at the active site and in positions that overlay with those for a correct base pair. The mismatch has Watson-Crick geometry consistent with a tautomeric or ionized base pair, with the pH dependence of misinsertion consistent with the latter. The results support the original idea that a base substitution can originate from a mismatch having Watson-Crick geometry, and they suggest a common catalytic mechanism for inserting a correct and an incorrect nucleotide. A second structure indicates that after misinsertion, the now primer-terminal G • T mismatch is also poised for catalysis but in the wobble conformation seen in other studies, indicating the dynamic nature of the pathway required to create a mismatch in fully duplex DNA.

PubMed: 21233421
DOI: 10.1073/pnas.1012825108

Experimental method

X-RAY DIFFRACTION (2 Å)