3C5G

Structure of a ternary complex of the R517K Pol lambda mutant

Summary for 3C5G

• Entry DOI: 10.2210/pdb3c5g/pdb
• Related: 3C5F
• Descriptor: DNA polymerase lambda, DNA (5'-D(*DCP*DGP*DGP*DCP*DAP*DAP*DTP*DAP*DCP*DTP*DG)-3'), DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*(2DT))-3'), ... (9 entities in total)
• Functional Keywords: helix-hairpin-helix, dna damage, dna repair, dna replication, dna synthesis, dna-binding, dna-directed dna polymerase, lyase, manganese, metal-binding, nucleotidyltransferase, nucleus, phosphoprotein, transferase, transferase/dna, lyase-dna complex, transferase-dna, lyase/dna
• Biological source: Homo sapiens (Human)
• Cellular location: Nucleus : Q9UGP5
• Total number of polymer chains: 8
• Total formula weight: 88814.92

Authors

Garcia-Diaz, M.,Bebenek, K.,Foley, M.C.,Pedersen, L.C.,Schlick, T.,Kunkel, T.A. (deposition date: 2008-01-31, release date: 2008-07-29, Last modification date: 2024-10-09)

Primary citation

Bebenek, K.,Garcia-Diaz, M.,Foley, M.C.,Pedersen, L.C.,Schlick, T.,Kunkel, T.A.
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.
Embo Rep., 9:459-464, 2008

PubMed Abstract: The simple deletion of nucleotides is common in many organisms. It can be advantageous when it activates genes beneficial to microbial survival in adverse environments, and deleterious when it mutates genes relevant to survival, cancer or degenerative diseases. The classical idea is that simple deletions arise by strand slippage. A prime opportunity for slippage occurs during DNA synthesis, but it remains unclear how slippage is controlled during a polymerization cycle. Here, we report crystal structures and molecular dynamics simulations of mutant derivatives of DNA polymerase lambda bound to a primer-template during strand slippage. Relative to the primer strand, the template strand is in multiple conformations, indicating intermediates on the pathway to deletion mutagenesis. Consistent with these intermediates, the mutant polymerases generate single-base deletions at high rates. The results indicate that dNTP-induced template strand repositioning during conformational rearrangements in the catalytic cycle is crucial to controlling the rate of strand slippage.

PubMed: 18369368
DOI: 10.1038/embor.2008.33

Experimental method

X-RAY DIFFRACTION (2.2 Å)