3K5M

Crystal structure of E.coli Pol II-abasic DNA-ddGTP Lt(-2, 2) ternary complex

Summary for 3K5M

• Entry DOI: 10.2210/pdb3k5m/pdb
• Related: 3K57 3K58 3K59 3K5A 3K5L 3K5N 3K5O
• Descriptor: DNA polymerase II, DNA (5'-D(*AP*GP*TP*CP*CP*TP*GP*(3DR)P*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3'), DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3'), ... (6 entities in total)
• Functional Keywords: dna damage, dna repair, dna-binding, dna-directed dna polymerase, nucleotidyltransferase, sos response, transferase, transferase-dna complex, transferase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 101033.55

Authors

Yang, W.,Wang, F. (deposition date: 2009-10-07, release date: 2010-02-02, Last modification date: 2023-09-06)

Primary citation

Wang, F.,Yang, W.
Structural insight into translesion synthesis by DNA Pol II.
Cell(Cambridge,Mass.), 139:1279-1289, 2009

PubMed Abstract: E. coli DNA Pol II and eukaryotic Rev3 are B-family polymerases that can extend primers past a damaged or mismatched site when the high-fidelity replicative polymerases in the same family are ineffective. We report here the biochemical and structural properties of DNA Pol II that facilitate this translesion synthesis. DNA Pol II can extend primers past lesions either directly or by template skipping, in which small protein cavities outside of the active site accommodate looped-out template nucleotides 1 or 2 bp upstream. Because of multiple looping-out alternatives, mutation spectra of bypass synthesis are complicated. Moreover, translesion synthesis is enhanced by altered partitioning of DNA substrate between the polymerase active site and the proofreading exonuclease site. Compared to the replicative B family polymerases, DNA Pol II has subtle amino acid changes remote from the active site that allow it to replicate normal DNA with high efficiency yet conduct translesion synthesis when needed.

PubMed: 20064374
DOI: 10.1016/j.cell.2009.11.043

Experimental method

X-RAY DIFFRACTION (2.04 Å)