Crystal Structure of an ATP-Dependent DNA Ligase from Bacteriophage T7

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Crystal Structure of an ATP-Dependent DNA Ligase from Bacteriophage T7 Hosahalli S. Subramanya, Aidan J. Doherty, Stephen R. Ashford, Dale B. Wigley Cell Volume 85, Issue 4, Pages 607-615 (May 1996) DOI: 10.1016/S0092-8674(00)81260-X

Figure 1 The Fold of T7 DNA Ligase (A) Stereo diagram illustrating the overall fold of T7 DNA ligase. Residue numbers are included to assist in following the path of the polypeptide chain. (B) Ribbon representation of the enzyme after removal of the first 130 amino acids at the N terminus (see text for explanation). These figures were prepared using the program PREPPI. Cell 1996 85, 607-615DOI: (10.1016/S0092-8674(00)81260-X)

Figure 2 Ribbon Diagram Illustrating the Domain Structure of the Protein The N-terminal domain (domain 1) is colored in green and the C-terminal domain (domain 2) in red. The bound ATP is overlaid in blue. This figure was prepared using the program RIBBONS (Carson 1991). Cell 1996 85, 607-615DOI: (10.1016/S0092-8674(00)81260-X)

Figure 3 The ATP-Binding Site Electron density for the bound ATP in a simulated annealing omit map (Fo-Fc) in which ATP was excluded from the model. The map is contoured at 2s, and the coordinates from the final model of the ATP complex have been overlaid for reference. Cell 1996 85, 607-615DOI: (10.1016/S0092-8674(00)81260-X)

Figure 4 The Motifs Conserved between DNA Ligase and Other Nucleotidyltransferases The motifs are shown at the top of the figure and their positions in the crystal structure of DNA ligase are indicated by the corresponding colors in the ribbon diagram below. The capping enzymes (CE), DNA ligases (DNA), RNA ligases (RNA) and tRNA ligases (tRNA) from vaccinia virus (Vac), Shope fibroma virus (SFV), African swine fever virus (ASF), Chlorella virus (PBCV) (Li et al. 1995), fowlpox virus (FPV), S. cerevisae (Sc), S. pombe (Sp), H. sapiens ligase I (Hu1), bacteriophages T4 (T4) and T7 (T7), and C. albicans (Ca) (Baymiller et al. 1994). The alignments are after Shuman and Schwer, 1995, and Kletzin, 1992, though the alignment in motif V has been slightly altered from that in Shuman and Schwer, 1995. Residues enclosed in boxes have been shown to be essential for activity; numbers adjoined by dashes represent the number of residues between the adjacent motifs. Cell 1996 85, 607-615DOI: (10.1016/S0092-8674(00)81260-X)

Figure 5 The Charge Distribution over the Surface of the Ligase Molecule The surface charge was calculated using the program GRASP (Nicholls and Honig 1991). Positive potential is shown in blue and negative potential in red. The bound ATP is indicated in green and the triphosphate tail of the coenzyme can be seen protruding from the binding pocket into the groove. The longest dimension of the molecule is 74 Å (essentially from left to right in this view). The depth and shape of the cleft is very similar to that observed for the HhaI and HaeIII methyltransferases (Klimasauskas et al. 1994; Reinisch et al. 1995). Cell 1996 85, 607-615DOI: (10.1016/S0092-8674(00)81260-X)

Figure 6 Proposed General Mechanism for Ligases and Related Nucleotidyltransferases Cell 1996 85, 607-615DOI: (10.1016/S0092-8674(00)81260-X)

Figure 7 Plot of Correlation Coefficient for the Electron Density in the Averaged Map and That Calculated for the Model for Each Residue in the structure Cell 1996 85, 607-615DOI: (10.1016/S0092-8674(00)81260-X)