ABSTRACT
The DNA ligase IV-Xrcc4 complex is responsible for the ligation of broken DNA ends in the non-homologous end-joining (NHEJ) pathway of DNA double strand break repair in mammals. Mutations in DNA ligase IV (Lig4) lead to immunodeficiency and radiosensitivity in humans. Only partial structural information for Lig4 and Xrcc4 is available, while the structure of the full-length proteins and their arrangement within the Lig4-Xrcc4 complex is unknown. The C-terminal domain of Xrcc4, whose structure has not been solved, contains phosphorylation sites for DNA-PKcs and is phylogenetically conserved, indicative of a regulatory role in NHEJ. Here, we have purified full length Xrcc4 and the Lig4-Xrcc4 complex, and analysed their structure by single-particle electron microscopy. The three-dimensional structure of Xrcc4 at a resolution of approximately 37A reveals that the C-terminus of Xrcc4 forms a dimeric globular domain connected to the N-terminus by a coiled-coil. The N- and C-terminal domains of Xrcc4 locate at opposite ends of an elongated molecule. The electron microscopy images of the Lig4-Xrcc4 complex were examined by two-dimensional image processing and a double-labelling strategy, identifying the site of the C-terminus of Xrcc4 and the catalytic core of Lig4 within the complex. The catalytic domains of Lig4 were found to be in the vicinity of the N-terminus of Xrcc4. We provide a first sight of the structural organization of the Lig4-Xrcc4 complex, which suggests that the BRCT domains could provide the link of the ligase to Xrcc4 while permitting some movements of the catalytic domains of Lig4. This arrangement may facilitate the ligation of diverse configurations of damaged DNA.
Subject(s)
DNA Ligases/metabolism , DNA Ligases/ultrastructure , DNA Repair , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/ultrastructure , DNA/metabolism , DNA Ligase ATP , DNA Ligases/genetics , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , Humans , Microscopy, Electron , Models, Molecular , Protein Binding , Protein Structure, Quaternary , Protein Structure, TertiaryABSTRACT
The 3D structure of the ternary complex, consisting of DNA ligase, the proliferating cell nuclear antigen (PCNA) clamp, and DNA, was investigated by single-particle analysis. This report presents the structural view, where the crescent-shaped DNA ligase with 3 distinct domains surrounds the central DNA duplex, encircled by the closed PCNA ring, thus forming a double-layer structure with dual contacts between the 2 proteins. The relative orientations of the DNA ligase domains, which remarkably differ from those of the known crystal structures, suggest that a large domain rearrangement occurs upon ternary complex formation. A second contact was found between the PCNA ring and the middle adenylation domain of the DNA ligase. Notably, the map revealed a substantial DNA tilt from the PCNA ring axis. This structure allows us to propose a switching mechanism for the replication factors operating on the PCNA ring.
Subject(s)
DNA Ligases/chemistry , DNA Replication , DNA/chemistry , Proliferating Cell Nuclear Antigen/chemistry , Pyrococcus furiosus/enzymology , Crystallography, X-Ray , DNA/ultrastructure , DNA Ligase ATP , DNA Ligases/ultrastructure , Microscopy, Electron , Models, Molecular , Nucleic Acid Conformation , Proliferating Cell Nuclear Antigen/ultrastructure , Static ElectricityABSTRACT
By using the atomic force microscope (AFM), three-dimensional structures of biological specimens may be imaged at nanometer resolution. Furthermore, samples can be imaged in air or in fluid environments. The tapping mode of AFM operation for imaging has offered a significant advance in visualizing soft biological structures, such as DNA, proteins, and membranes. Here, we review the principles underlying the application of this instrument to radiation biological investigations. We focus on examples of proteins involved in the processes of repair of damaged DNA, including poly(ADP-ribose) polymerase, Ku protein, and DNA protein kinase. Novel observations on the character of DNA damage and repair have been addressed by direct visualization of DNA and protein-DNA interactions, such as the observation that the Ku protein is capable of physically joining DNA fragments in vitro. The AFM offers a powerful tool for investigating biologically important molecular interactions that are relevant to DNA damage and repair processes.
