8EFC

Structure of Lates calcarifer DNA polymerase theta polymerase domain with long duplex DNA, complex Ia

Summary for 8EFC

• Entry DOI: 10.2210/pdb8efc/pdb
• EMDB information: 28078
• Descriptor: DNA polymerase theta, DNA (5'-D(*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*CP*CP*TP*CP*AP*CP*AP*G)-3'), DNA (5'-D(*AP*CP*TP*GP*TP*GP*AP*GP*GP*CP*AP*TP*CP*CP*GP*TP*AP*GP*(2DA))-3'), ... (5 entities in total)
• Functional Keywords: dna double-strand break repair, microhomology-mediated end joining, dna binding protein
• Biological source: Lates calcarifer; More
• Total number of polymer chains: 3
• Total formula weight: 110955.13

Authors

Li, C.,Zhu, H.,Sun, J.,Gao, Y. (deposition date: 2022-09-08, release date: 2022-12-14, Last modification date: 2025-05-21)

Primary citation

Li, C.,Zhu, H.,Jin, S.,Maksoud, L.M.,Jain, N.,Sun, J.,Gao, Y.
Structural basis of DNA polymerase theta mediated DNA end joining.
Nucleic Acids Res., 51:463-474, 2023

PubMed Abstract: DNA polymerase θ (Pol θ) plays an essential role in the microhomology-mediated end joining (MMEJ) pathway for repairing DNA double-strand breaks. However, the mechanisms by which Pol θ recognizes microhomologous DNA ends and performs low-fidelity DNA synthesis remain unclear. Here, we present cryo-electron microscope structures of the polymerase domain of Lates calcarifer Pol θ with long and short duplex DNA at up to 2.4 Å resolution. Interestingly, Pol θ binds to long and short DNA substrates similarly, with extensive interactions around the active site. Moreover, Pol θ shares a similar active site as high-fidelity A-family polymerases with its finger domain well-closed but differs in having hydrophilic residues surrounding the nascent base pair. Computational simulations and mutagenesis studies suggest that the unique insertion loops of Pol θ help to stabilize short DNA binding and assemble the active site for MMEJ repair. Taken together, our results illustrate the structural basis of Pol θ-mediated MMEJ.

PubMed: 36583344
DOI: 10.1093/nar/gkac1201

Experimental method

ELECTRON MICROSCOPY (2.8 Å)