2P5O

Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog

Replaces:  1RV2

Summary for 2P5O

• Entry DOI: 10.2210/pdb2p5o/pdb
• Related: 1CLQ 1IG9 1Q9Y 2DTU 2DY4
• Descriptor: Template DNA, Primer DNA, DNA polymerase, ... (4 entities in total)
• Functional Keywords: dna polymerase, abasic site, dna lesion, exonuclease switch, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage RB69; More
• Total number of polymer chains: 12
• Total formula weight: 463320.20

Authors

Hogg, M.,Wallace, S.S.,Doublie, S. (deposition date: 2007-03-15, release date: 2007-04-03, Last modification date: 2024-11-13)

Primary citation

Hogg, M.,Wallace, S.S.,Doublie, S.
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.
Embo J., 23:1483-1493, 2004

PubMed Abstract: Abasic sites are common DNA lesions, which are strong blocks to replicative polymerases and are potentially mutagenic when bypassed. We report here the 2.8 A structure of the bacteriophage RB69 replicative DNA polymerase attempting to process an abasic site analog. Four different complexes were captured in the crystal asymmetric unit: two have DNA in the polymerase active site whereas the other two molecules are in the exonuclease mode. When compared to complexes with undamaged DNA, the DNA surrounding the abasic site reveals distinct changes suggesting why the lesion is so poorly bypassed: the DNA in the polymerase active site has not translocated and is therefore stalled, precluding extension. All four molecules exhibit conformations that differ from the previously published structures. The polymerase incorporates dAMP across the lesion under crystallization conditions, indicating that the different conformations observed in the crystal may be part of the active site switching reaction pathway.

PubMed: 15057283
DOI: 10.1038/sj.emboj.760015

Experimental method

X-RAY DIFFRACTION (2.8 Å)