The novel closed structure of an archaeal DNA ligase from Pyrococcus furiosus
Kosuke Morikawa, H. Nishida, S. Kiyonari, Y. Ishino

DNA ligases join single-strand breaks in double-stranded DNA, and are essential to maintain genome integrity in DNA metabolism. Here, we report the 1.8 Å resolution crystal structure of Pyrococcus furiosus DNA ligase (PfuLig), which presents the first full-length atomic view of an ATP-dependent eukaryotic type enzyme. It comprises the N-terminal DNA binding domain, the middle adenylation domain, and the C-terminal OB-fold domain. The architectures of each domain resemble those of human DNA ligase I, but the domain arrangements are strikingly different between the two enzymes. The closed conformation of the two “catalytic core” domains at the carboxy terminus in PfuLig creates a small compartment, which holds a non-covalently bound AMP. This domain rearrangement results from the “domain-connecting” role of the C-terminal extension commonly found in archaeal and eukaryotic DNA ligases, suggesting that the ligation reaction could be completed by the replacement of the motif VI within the OB-fold domain with nicked substrate DNA. This structural rearrangement may contribute to protecting the AMP bound to the enzyme from its diffusing out until it encounters substrate DNA.