. Another dual co-factor specificity exists in the archaeal DNA ligases, which use ADP as well as ATP, as found in the enzymes from A. pernix and Staphylothermus marinus , and in the case of Sulfobococcus zilligii, GTP is also the functional cofactor. The DNA ligases from P. horikoshii and P. furiosus have a strict ATP preference. biochemical data have not been obtained to resolve the issue of dual co-factor specificity, and further biochemical and structural analyses are required. The crystal structure of P. furiosus DNA ligase was solved and the physical and functional interactions between the DNA ligase and PCNA was shown. The detailed interaction mode between human Lig I and PCNA is somewhat unclear, because of several controversial reports. stimulatory effect of P. furiosus PCNA on the enzyme activity of the cognate DNA ligase was observed at a high salt concentration, at which a DNA ligase alone cannot bind to a nicked DNA substrate. Interestingly, the PCNA-binding site is located in the middle of the N-terminal DNA binding domain (DBD) of the P. furiosus DNA ligase, and the binding motif, QKSFF, which is proposed as a shorter version of the PIP box, is actually looped out from the protein surface. Interestingly, this motif is located in the middle of the protein chain, rather than the N-or C-terminal region, where the PIP boxes are usually located. To confirm that this motif is conserved in the archaeal / eukaryotic DNA ligases, the physical and functional interactions between A. pernix DNA ligase and PCNA was analyzed and the interaction was shown to mainly depend on the phenylalanine 132 residue, which is located in the predicted region from the multiple sequence alignment of the ATP-dependent DNA ligases. crystal structure of the human Lig I, complexed with DNA, was solved as the first ATPdependent mammalian DNA ligase, although the ligase was an N-terminal truncated form. The structure comprises the N-terminal DNA binding domain, the middle adenylation domain, and the C-terminal OB-fold domain. The crystal structure of Lig I (residues 233 to 919) in complex with a nicked, 5'-adenylated DNA intermediate revealed that the enzyme redirects the path of the dsDNA, to expose the nick termini for the strand-joining reaction. The N-terminal DNA-binding domain works to encircle the DNA substrate like PCNA and to stabilize the DNA in a distorted structure, positioning the catalytic core on the nick. crystal structure of the full length DNA ligase from P. furiosus revealed that the architecture of each domain resembles those of Lig I, but the domain arrangements strikingly differ between the two enzymes. This domain rearrangement is probably derived from the domain-connecting role of the helical extension conserved at the C-termini in the archaeal and eukaryotic DNA ligases. The DNA substrate in the open form of Lig I is replaced by motif VI at the C-terminus, in the closed form of P. furiosus DNA ligase. the shapes and electrostatic distributions are similar between motif VI and the DNA substrate, suggesting that motif VI in the closed state mimics the incoming substrate DNA. The subsequently solved crystal structure of ...
