Volume 25, Issue 6, Pages 943-949 (March 2007) The Structure of the ATPase that Powers DNA Packaging into Bacteriophage T4 Procapsids  Siyang Sun, Kiran Kondabagil, Petra M. Gentz, Michael G. Rossmann, Venigalla B. Rao  Molecular Cell  Volume 25, Issue 6, Pages 943-949 (March 2007) DOI: 10.1016/j.molcel.2007.02.013 Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 1 The T4 DNA-Packaging Machine (A) A schematic diagram shows the T4 procapsid while being filled with DNA. The portal protein, gp20, forms a dodecameric head-tail connector through which the genome enters the procapsid and exits the mature phage. The stoichiometry of the large terminase gp17 oligomer is suggested to be pentameric or decameric. The amino-terminal domain of gp17 has ATPase activity, whereas the carboxy-terminal domain has nuclease activity. There are probably eight to ten gp16 monomers in the small terminase oligomer. The small terminase functions to enhance the ATPase activity of the large terminase. (B) A ribbon diagram shows the gp17 N360-ED mutant structure. Subdomain I consists of the nucleotide-binding motif (Rossmann et al., 1974). The strands in the β sheet (colored, in sequence, red, orange, yellow, green, cyan, and blue) follow a 324516 topology, as in most other translocating ATPases. The ATP molecule is colored purple. The loop associated with adenine binding (purple) changes its conformation in the apo structure (yellow). The conserved ATP-binding subdomain I is spatially distinct. The N and C termini of gp17 N360-ED that form subdomain II may be a part of the C-terminal nuclease domain of gp17. The figure was generated with the PyMOL program (DeLano, 2002). Molecular Cell 2007 25, 943-949DOI: (10.1016/j.molcel.2007.02.013) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 2 The Active Center of the gp17 ATPase (A) Stereodiagram of the ATP-binding pocket in the gp17 N360-ED mutant showing residues that interact with ATP (the figure was generated with the PyMOL program [DeLano, 2002]). Schematic drawing of the ATP-binding pocket in gp17 N360 (B) observed in the ED mutant, (C) before hydrolysis, and (D) after hydrolysis. The ATP, ADP, and Pi molecules are colored red, the catalytic residues are purple, the Mg2+ and water molecules are green, and the residues that bind the AMP fragment of ATP are black. K166 and T167 are part of the Walker A phosphate-binding “P” loop, and D255 belongs to the Walker B motif. Based on studies on homologous ATPases (Abrahams et al., 1994; Soultanas et al., 1999), E256, the catalytic Glu, activates a water molecule for nucleophilic attack on the pyrophosphate bond as shown in (C) (Subramanya et al., 1996). The γ phosphate is then stabilized by R162, the “switch residue,” in a pentacoordinated transition state to facilitate the leaving of Pi after hydrolysis. In the ED mutant, K166 interacts with the mutated Walker B E255 instead of the β and γ phosphates, and therefore Mg2+ and the two waters are not seen in the ED mutant structure. (E) The best Cα backbone superposition of gp17 N360-ED onto the monomeric helicase PcrA is shown in a stereodiagram. Note the superposition of the catalytic residues of N360 (red) and PcrA (blue). Molecular Cell 2007 25, 943-949DOI: (10.1016/j.molcel.2007.02.013) Copyright © 2007 Elsevier Inc. Terms and Conditions