9NPU

Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate containing template ribonucleotide opposite primer terminus, and incoming dUMPNPP

Summary for 9NPU

• Entry DOI: 10.2210/pdb9npu/pdb
• Descriptor: DNA polymerase lambda, CHLORIDE ION, DNA/RNA (5'-D(*CP*GP*GP*CP*A)-R(P*G)-D(P*TP*AP*CP*TP*G)-3'), ... (11 entities in total)
• Functional Keywords: family x polymerase, nonhomologous end joining, transferase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 45784.64

Authors

Kaminski, A.M.,Luthman, A.J.,Pedersen, L.C.,Ramsden, D.A.,Kunkel, T.A. (deposition date: 2025-03-11, release date: 2026-01-21)

Primary citation

Luthman, A.J.,Chiruvella, K.K.,Kaminski, A.M.,Kunkel, T.A.,Pedersen, L.C.,Ramsden, D.A.
Nonhomologous end-joining uses distinct mechanisms to repair each strand of a double strand break.
Nat Commun, 16:11599-11599, 2025

PubMed Abstract: Nonhomologous end-joining repairs chromosomal double strand breaks, but it is unknown whether both strands are repaired by this pathway, and if one strand break's repair path impacts the other. Here, we show that nonhomologous end-joining employs both of two a priori possible strategies. Strand breaks that can be directly ligated are joined near-simultaneously, with no effect of one strand break's repair path on the other. More complex end structures require obligatorily ordered repair. The first strand to be repaired is used as template for repair of the opposite/second strand break, with the latter repair reaction occurring fastest when also coupled to nonhomologous end-joining. Enforced asymmetry in repair of each strand break can extend to the gap-filling polymerase employed, and whether the polymerases incorporate RNA or DNA. Our results resolve questions about pathway mechanism and identify a requirement for flexibility of the nonhomologous end-joining machinery for efficient repair of both strand breaks within diverse cellular double strand breaks.

PubMed: 41285786
DOI: 10.1038/s41467-025-66528-8

Experimental method

X-RAY DIFFRACTION (1.63 Å)