1N56

Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion

Summary for 1N56

• Entry DOI: 10.2210/pdb1n56/pdb
• Related: 1JX4 1JXL 1N48
• Descriptor: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3', 5'-D(*TP*CP*AP*TP*(3DR)P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', DNA polymerase IV, ... (7 entities in total)
• Functional Keywords: y-family, dna polymerase, dna lesion bypass, protein-dna complex, transferase-dna complex, transferase/dna
• Biological source: Sulfolobus solfataricus; More
• Cellular location: Cytoplasm (Probable): Q97W02
• Total number of polymer chains: 6
• Total formula weight: 100331.25

Authors

Ling, H.,Boudsocq, F.,Woodgate, R.,Yang, W. (deposition date: 2002-11-04, release date: 2004-02-24, Last modification date: 2023-10-25)

Primary citation

Ling, H.,Boudsocq, F.,Woodgate, R.,Yang, W.
Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.
Mol.Cell, 13:751-762, 2004

PubMed Abstract: Dpo4 from S. Solfataricus, a DinB-like Y family polymerase, efficiently replicates DNA past an abasic lesion. We have determined crystal structures of Dpo4 complexed with five different abasic site-containing DNA substrates and find that translesion synthesis is template directed with the abasic site looped out and the incoming nucleotide is opposite the base 5' to the lesion. The ensuing DNA synthesis generates a -1 frameshift when the abasic site remains extrahelical. Template realignment during primer extension is also observed, resulting in base substitutions or even +1 frameshifts. In the case of a +1 frameshift, the extra nucleotide is accommodated in the solvent-exposed minor groove. In addition, the structure of an unproductive Dpo4 ternary complex suggests that the flexible little finger domain facilitates DNA orientation and translocation during translesion synthesis.

PubMed: 15023344
DOI: 10.1016/s1097-2765(04)00101-7

Experimental method

X-RAY DIFFRACTION (2.4 Å)