Volume 6, Issue 6, Pages 1461-1472 (December 2000) Crystal Structure of the Hexameric Traffic ATPase of the Helicobacter pylori Type IV Secretion System  Hye-Jeong Yeo, Savvas N Savvides, Andrew B Herr, Erich Lanka, Gabriel Waksman  Molecular Cell  Volume 6, Issue 6, Pages 1461-1472 (December 2000) DOI: 10.1016/S1097-2765(00)00142-8

Figure 1 Structure of the HP0525–ADP Complex (A) Representative region (the β6 strand) of the experimental electron density at 3 Å resolution. The electron density results from a map calculated using SAD phases after NCS averaging and solvent flipping and is contoured at a 2σ level. The final refined model is shown in stick representation color-coded in yellow for carbon, blue for nitrogen, and red for oxygen. (B) Stereo ribbon diagram of the structure of HP0525 bound to ADP and a 9-mer of PEG (Carson 1997). α helices, 310 helices, strands, and loops are indicated in blue, dark blue, green, and amber, respectively. The ADP is in magenta, and the PEG molecule is in gray. Secondary structural elements (except for the 310 helices) are labeled from β1 to β13, while helices are labeled from αA to αI. N and C indicate the N and C termini of the protein, respectively. Molecular Cell 2000 6, 1461-1472DOI: (10.1016/S1097-2765(00)00142-8)

Figure 2 Sequence Alignment of the VirB11 ATPases and Location of Secondary Structures in H. pylori HP0525 The following sequences were used in the alignment: HP0525 from H. pylori, LvhB11 from L. pneumophila, VirB11 from A. tumefaciens, TrbB from plasmid RP4, and TraG from plasmid pKM101. Strictly conserved residues are shown in green boxes, while residues that are conservatively substituted are shown in pink boxes. Amino acid numbering at the top refers to HP0525. Numbering at the end of the lines refers to the number of the last amino acid shown at the end of the line in the corresponding sequence. Secondary structural elements of HP0525 are shown at the bottom with helices and strands indicated as cylinders and arrows, respectively. 310 helices are not shown for clarity. Residues involved in subunit–subunit interactions are shown in blue boxes. Residues involved in ADP binding and proposed to be involved in ATP binding and hydrolysis are boxed in red. Molecular Cell 2000 6, 1461-1472DOI: (10.1016/S1097-2765(00)00142-8)

Figure 3 Ribbon Diagrams of the HP0525 Hexamer In (A), (B), and (D), each HP0525 subunit is color-coded differently. Each is represented in ribbon diagram as in Figure 1B. Note that the subunit in yellow in (D) is in the same orientation as in Figure 1B. ADP is shown in magenta, while PEG is shown in gray. In (C), each subunit is in the same color, with the N-terminal domain colored in gold and the C-terminal domain colored in magenta. In (C), the ADP is shown in dark blue and the PEG is cyan. (A) Stereo ribbon diagram of HP0525 viewed down the large hole formed by the N-terminal domains (Carson 1997). (B) Stereo ribbon diagram of HP0525 viewed from the side. This view is obtained by rotating the HP0525 shown in (A) 90° clockwise along the vertical axis of (A). (C) Ribbon diagram of HP0525 in the same orientation as (B). The color coding of the subunit illustrates the double-ring structure of HP0525. The labeling above the panel indicates the putative location of the surfaces spanning the inner membrane (IM) or exposed to the cytoplasm (Cyt). (D) Stereo ribbon diagram of HP0525 viewed down the small hole at the base of the grapple formed by the tips of the C-terminal domains. Molecular Cell 2000 6, 1461-1472DOI: (10.1016/S1097-2765(00)00142-8)

Figure 4 Surface of the HP0525–ADP Complex The surfaces were contoured and displayed using the program GRASP (Nicholls et al. 1991). Color coding is according to charge, blue for the most positive regions and red for most negative regions with linear interpolation in between. (A) Surface of the HP0525–ADP complex viewed down the large hole. This view corresponds to that of Figure 3A. The inside and outside dimensions of the HP0525 chamber are indicated in yellow. (B) Surface of the HP0525–ADP complex viewed from the side. Top, the entire HP0525 hexamer. This view corresponds to that shown in Figure 3B and Figure 3C. The putative location of the membrane-spanning and cytoplasm-exposed regions of the HP0525 hexamer are indicated. Also three 9-mer PEG molecules and two ADP molecules are clearly visible and shown as ball-and-stick representation (white for carbon, red for oxygen, yellow for phosphorus, and blue for nitrogen) and labeled accordingly as PEG and ADP. Bottom, cut-away of the HP0525 hexamer. The orientation is the same as in the top. Four subunits are shown, which allow to visualize the surface potential inside the HP0525 chamber. The inside and outside dimensions of the HP0525 chamber are indicated in yellow. (C) Surface of the HP0525–ADP complex viewed down the small hole of the chamber. Molecular Cell 2000 6, 1461-1472DOI: (10.1016/S1097-2765(00)00142-8)

Figure 5 The Subunit–Subunit Interface of the HP0525 Hexamer In (A) through (D), the two subunits are color-coded red and yellow, respectively, and represented as ribbons as in Figure 3A. Secondary structural elements are labeled according to the nomenclature defined in Figure 1B. (A) Overview of the subunit–subunit interface (Carson 1997). Residues involved in interactions between subunits are shown in ball-and-stick representation with residues responsible for contacts between N-terminal domains indicated in green, residues involved in interactions between the N-terminal domain of one subunit and the C-terminal domain of the other subunit indicated in cyan, and the residues involved in contacts between C-terminal domains indicated in magenta. (B) Stereo diagram of the interface between N-terminal domains (the region indicated in green in [A]). Residues are in ball-and-stick representation color-coded gray for carbons, red for oxygen, blue for nitrogen, and green for sulfur. Residues are labeled, as are the few of the secondary structural elements shown. (C) Stereo diagram of the interface between N-terminal and C-terminal domains of adjacent subunits (the region indicated in cyan in [A]). Residues are shown and labeled as in (B). ADP is shown in ball-and-stick representation color coded in magenta. The black circle locates a large cluster of arginine residues believed to destabilize the interface in the absence of nucleotide. (D) Stereo diagram of the interface between C-terminal domains (the region indicated in magenta in [A]). Residues are shown and labeled as in (B). Molecular Cell 2000 6, 1461-1472DOI: (10.1016/S1097-2765(00)00142-8)

Figure 6 The Nucleotide Binding Site (A) Interaction diagram between the ADP (in magenta) and the protein (in black). Residues involved are labeled. Interactions are indicated by dashed lines with distances between atoms involved in the interactions indicated in angstroms. (B) Stereo ribbon diagram of the ADP–protein interactions (Carson 1997). The protein is represented as a red ribbon with secondary structures defined as in Figure 1B. The ADP is in magenta. Residues involved in interactions are in ball-and-stick representation color coded as in Figure 5B. Two residues, Glu-248 and Glu-209, are shown in pink. These residues do not interact with ADP; however, their positions within the nucleotide binding site suggest that they act as catalysts for ATP hydrolysis. Molecular Cell 2000 6, 1461-1472DOI: (10.1016/S1097-2765(00)00142-8)

Figure 7 Schematic Model for the Opening and Closure of the HP0525 Chamber The N-terminal and C-terminal domains are represented in dark and light blue, respectively. The view is down the big hole as in Figure 3A. ATP molecules are indicated as yellow balls. Molecular Cell 2000 6, 1461-1472DOI: (10.1016/S1097-2765(00)00142-8)