Nonhomologous end joining repairs DNA double-strand breaks created by ionizing radiation and V(D)J recombination. Ku, XRCC4/Ligase IV (XL) and XLF have a remarkable mismatched end (MEnd) ligase activity, particularly for ends with mismatched 3' overhangs, but the mechanism has remained obscure. Here, we showed XL required Ku to bind DNA, while XLF required both Ku and XL to bind DNA. We detected cooperative assembly of one or two Ku molecules and up to 5 molecules each of XL and XLF into a Ku:XL:XLF-DNA (MEnd ligase-DNA) complex. XLF mutations that disrupted its interactions with XRCC4 or DNA also disrupted complex assembly and end joining. Together with published co-crystal structures of truncated XRCC4 and XLF proteins, our data with full-length Ku, XL and XLF bound to DNA indicate assembly of a filament containing Ku plus alternating XL and XLF molecules. By contrast, in the absence of XLF, we detected cooperative assembly of up to 6 molecules each of Ku and XL into a Ku:XL-DNA complex, consistent with a filament containing alternating Ku and XL molecules. Despite a lower molecular weight, MEnd ligase-DNA had a lower electrophoretic mobility than Ku:XL-DNA. The anomalous difference in mobility and difference in XL to Ku molar ratio suggest that MEnd ligase-DNA has a distinct structure that successfully aligns mismatched DNA ends for ligation.
View details for DOI 10.1074/jbc.M113.464115
View details for Web of Science ID 000320721900017
View details for PubMedID 23620595