1ZJM

Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus

Summary for 1ZJM

• Entry DOI: 10.2210/pdb1zjm/pdb
• Related: 1BPX
• Descriptor: d(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... (6 entities in total)
• Functional Keywords: nucleotidyltransferase, dna repair, dna mismatch, base excision repair, dna-lyase-transferase complex, dna/lyase/transferase
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P06746
• Total number of polymer chains: 4
• Total formula weight: 47744.84

Authors

Batra, V.K.,Beard, W.A.,Shock, D.D.,Pedersen, L.C.,Wilson, S.H. (deposition date: 2005-04-29, release date: 2005-08-16, Last modification date: 2023-08-23)

Primary citation

Batra, V.K.,Beard, W.A.,Shock, D.D.,Pedersen, L.C.,Wilson, S.H.
Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.
STRUCTURE, 13:1225-1233, 2005

PubMed Abstract: DNA polymerases occasionally insert the wrong nucleotide. For this error to become a mutation, the mispair must be extended. We report a structure of DNA polymerase beta (pol beta) with a DNA mismatch at the boundary of the polymerase active site. The structure of this complex indicates that the templating adenine of the mispair stacks with the primer terminus adenine while the templating (coding) cytosine is flipped out of the DNA helix. Soaking the crystals of the binary complex with dGTP resulted in crystals of a ternary substrate complex. In this case, the templating cytosine is observed within the DNA helix and forms Watson-Crick hydrogen bonds with the incoming dGTP. The adenine at the primer terminus has rotated into a syn-conformation to interact with the opposite adenine in a planar configuration. Yet, the 3'-hydroxyl on the primer terminus is out of position for efficient nucleotide insertion.

PubMed: 16084394
DOI: 10.1016/j.str.2005.05.010

Experimental method

X-RAY DIFFRACTION (2.1 Å)