Volume 34, Issue 3, Pages 375-386 (May 2009) Crystallographic Insights into the Autocatalytic Assembly Mechanism of a Bacteriophage Tail Spike  Ye Xiang, Petr G. Leiman, Long Li, Shelley Grimes, Dwight L. Anderson, Michael G. Rossmann  Molecular Cell  Volume 34, Issue 3, Pages 375-386 (May 2009) DOI: 10.1016/j.molcel.2009.04.009 Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 1 Diagram of the Bacteriophage ϕ29 Tail Showing Its Structural Components (Left) A central section. (Right) A surface-rendered presentation. The 12 appendages (blue) are labeled 1–12. Note that appendages 1 and 6 are in the “up” position, whereas the others are in a “down” position (Xiang et al., 2006). Molecular Cell 2009 34, 375-386DOI: (10.1016/j.molcel.2009.04.009) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 2 Expression of gp12 Constructs (A) Diagram showing all the constructs that are reported in this paper. (B) SDS-PAGE gels showing the expression of all the gp12 constructs. The symbols + and − indicate the induced and uninduced cells. Molecular Cell 2009 34, 375-386DOI: (10.1016/j.molcel.2009.04.009) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 3 PAGE Gels Showing the Oligomeric States and Poly(Glycerol Phosphate)-Degrading Enzymatic Activities of gp12 and gp12 Mutants (A) A 10% SDS-PAGE gel showing the purified gp12 proteins. (B) A 8% SDS-PAGE gel showing the SDS-resistant oligomers formed by gp12 and gp12 mutants. (C) Native 15% PAGE gels showing the glycosylated poly(glycerol phosphate) after being treated with gp12 proteins. Molecular Cell 2009 34, 375-386DOI: (10.1016/j.molcel.2009.04.009) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 4 The Structures of gp12 Pre- and Postmaturation (A) Ribbon stereodiagram of gp12 trimer pre- and postmaturation with the three polypeptide chains shown in blue, green, and orange, respectively. The N and C termini of each polypeptide chain are marked with blue and red balls, respectively. Residues Tyr737 and Tyr744 of the D4 domain are shown in sticks and colored according to the corresponding polypeptide chain color. The self-cleavage sites in the three premature polypeptide chains are marked by black balls. The bound ATP molecules are shown in domain D4 of the premature structure with N, C, P, and O atoms colored blue, gray, yellow, and red, respectively. (B) Stereodiagram showing the conformational changes in the long loop of a D4 monomer in different states. The three parts of the long loop are colored in green, purple, and yellow. The bound ATP molecule is shown colored the same as in (A). The 3-fold axis of the D4 trimer is indicated by a black line. Molecular Cell 2009 34, 375-386DOI: (10.1016/j.molcel.2009.04.009) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 5 The Self-Proteolysis Mechanism of D4 and the Bound ATP Molecules in the Premature D4 Domain (A) Stereodiagram showing the self-proteolysis mechanism of D4. A part of the three polypeptide chains is shown in ribbon representation. Each of the three polypeptide chains is identified by a different color. Residues Ser691, Asp692, and Glu/Gln695 are shown as a ball-and-stick presentation with N, O, and C atoms colored in blue, red, and the corresponding polypeptide chain color, respectively. The cleavage sites in the uncleaved protein are indicated by arrows. (B) Stereodiagram showing a bound ATP molecule in the D4 domain. Part of the polypeptide chains in D4 is shown as ribbons and colored green in one polypeptide chain and is orange in a neighboring polypeptide chain. The bound ATP and the magnesium ion are shown as a ball-and-stick representation, with C, N, O, P, and Mg atoms colored in gray, blue, red, orange, and magenta, respectively. The electron density shown is of a (Fo − Fc) map contoured at 3 σ. Residues coordinating the ATP molecule are shown in a ball-and-stick representation, with N, O, and C atoms colored in blue, red, and green, respectively. The two glutamic acid residues that may be involved in the ATP hydrolysis are shown as a ball-and-stick representation with C atoms colored in purple. The self-cleavage site in a near neighboring molecule is colored in yellow and is marked by a black ball. (C) A bioluminescent assay showing the presence of ATP in the E695Q mutant protein. In row a, 1–5 shows the luminescence emission from ∼10 μM of boiled D4, D1∗-D2-D3, and E695Q; not boiled E695Q; and water, respectively. Row b shows the ATP standards with decreasing concentrations of 70, 50, 20, 10, and 5 μM from b1 to b5. Molecular Cell 2009 34, 375-386DOI: (10.1016/j.molcel.2009.04.009) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 6 Sequence Alignment of gp12 D4, Bacteriophage Tailspike Proteins Shown are Vp260 and Vp260-like proteins from PBCV-like viruses and bacterial adhesins. The secondary structural elements of gp12 D4 are shown above the alignments (arrows indicate β strands, and coils indicate α helices). Residues essential for ATP binding and hydrolysis are indicated by black and gray triangles, respectively. Residues essential for the self-proteolysis are indicated by stars. Completely conserved residues are shown in white on a gray background. Molecular Cell 2009 34, 375-386DOI: (10.1016/j.molcel.2009.04.009) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 7 The Poly(Glycerol-Phosphate)-Degrading Active Center of gp12 (A) Stereodiagram showing a bound CHES molecule near the two metal ions of the active center. Part of the protein backbone is shown as a ribbon representation colored in blue. Residue side chains, water molecules, the two bound metal ions, and the bound CHES molecule are shown as a ball-and-stick representation. C, N, O, and S atoms are colored in gray, blue, red, and yellow, respectively. The C atoms of the bound CHES molecule are colored in orange. The Ca2+ and Mg2+ ions are colored in cyan and green, respectively. The electron density is a (Fo − Fc) map contoured at 3 σ. (B) Stereodiagram showing two Co ions in the active center. The two Co ions are shown as balls and colored in magenta. The protein backbone, water molecules, and side chains are drawn and colored the same as in (A). The electron density shown is an anomalous difference map contoured at 8 σ. (C) Stereodiagram showing two CHES molecules in the substrate-binding groove of gp12. The protein surface is colored radially from gray (small radius) to black (large radius). The CHES molecules and the metal ions are drawn and colored the same as in (A). Molecular Cell 2009 34, 375-386DOI: (10.1016/j.molcel.2009.04.009) Copyright © 2009 Elsevier Inc. Terms and Conditions