Volume 16, Issue 5, Pages 766-775 (May 2008) An Intersubunit Active Site between Supercoiled Parallel β Helices in the Trimeric Tailspike Endorhamnosidase of Shigella flexneri Phage Sf6  Jürgen J. Müller, Stefanie Barbirz, Karolin Heinle, Alexander Freiberg, Robert Seckler, Udo Heinemann  Structure  Volume 16, Issue 5, Pages 766-775 (May 2008) DOI: 10.1016/j.str.2008.01.019 Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 1 Stereo Views of the Crystal Structure of the Sf6 TSPΔN Monomer and Trimer The N-terminal region, the β-helix domain, and the C-terminal domain of the monomer (A) are displayed in different shades of blue. In the trimer (B), chains are identified by different color. All figures representing structures were prepared using MOLSCRIPT (Kraulis, 1991) and BOBSCRIPT (Esnouf, 1997) in combination with RASTER3D (Merritt and Murphy, 1994). Structure 2008 16, 766-775DOI: (10.1016/j.str.2008.01.019) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 2 Structural Comparison of Sf6 TSP and P22 TSP Crystal structures of the monomers and biologically active trimers of Sf6 TSPΔN (A and C), and of P22 TSPΔN (B and D) (PDB code: 1TSP [Steinbacher et al., 1994]). The view is perpendicular to the trimer axis onto the intersubunit cleft (rotated by ∼45° relative to Figure 1). Structure 2008 16, 766-775DOI: (10.1016/j.str.2008.01.019) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 3 Architecture of the β-Helix Domain of Sf6 TSP (A) Minimal helix definition according to Yoder et al. (1993b), B1–B3 are β strands, T1–T3 are turns. (B) Cα trace of the minimal helices 3–14, view along the Sf6 TSPΔN trimer axis. The three individual β sheets are labeled b1, b2, and b3, and the stacked turns connecting strands B2 and B3 are labeled t2. (C) Stereo view of the Cα trace of the β-helix domain of Sf6 TSP superimposed onto P22 TSPΔN (thin black trace). (D) Structure-based sequence alignment of β-helix rungs of Sf6 TSP. Colors are as in (A–C). Residue side chains are marked “i” if they point into the β helix and “o” if they point outward. Structure 2008 16, 766-775DOI: (10.1016/j.str.2008.01.019) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 4 Left-Handed, Coiled-β-Coil Structure Formed by the Right-Handed β Helix (A) The Cα trace of the minimal helix within the monomeric β-helix domain was fitted by a least-squares method to an elliptical superhelix model with a superpitch of about 340 Å, a minor pitch of 4.72 Å, and a twist angle of about 5° per rung; view perpendicular to the β-helix axis. (B) View along the β-helix axis. (C) Coiled-β-coil model, constructed from 7 × 14 rungs of the trimeric β helix. Two chains are drawn as space-filling models, and one chain as Cα trace. Structure 2008 16, 766-775DOI: (10.1016/j.str.2008.01.019) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 5 Structural Homologs of the Sf6 TSP C-Terminal β Sandwich Domain, Seen in Blue (A) Superposition onto the rat μ2 adaptin domain (1BXX; rmsd, 1.8 Å for 51 matching Cα positions). (B) Superposition onto the capsid protein from African horse sickness virus (1AHS; rmsd, 1.9 Å for 51 matching Cα positions). (C) Topology diagrams from TOPS (Michalopoulos et al., 2004) for Sf6 TSP (left) and the African horse sickness virus capsid protein (right). α Helices and β strands are viewed end-on and indicated by circles and triangles, respectively. Their direction can be deduced from the connecting lines. Structure 2008 16, 766-775DOI: (10.1016/j.str.2008.01.019) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 6 Localization of the Endorhamnosidase Active Site of Sf6 TSPΔN (A) Difference electron density (contoured at 3σ) observed in a complex of the protein with one repeating unit (RU) of an O-antigen hydrolysis product (α-l-Rhap-(1-3)-β-l-GlcpNAc-(1-2)-α-l-Rhap-(1-2)-α-l-Rhap). The sugar points upwards to the N terminus of Sf6 TSP with its nonreducing end. Glu293 (chain C) and Asp247 (chain A) belong to the binding site. (B) Kinetics of hydrolysis of a fluorescence-labeled dodecasaccharide (3 RU, 2 μM) with 0.36 μM Sf6 TSPΔN wild-type (closed triangles) and mutants D247N (closed diamonds), E293Q (closed squares), E366Q (closed circles) and D399N (open circles) at 15°C, as determined by HPLC (Freiberg et al., 2003). See Table 1 for kcat/KM values calculated from these data. (C) An octasaccharide (2 RU) modeled into the binding site with its reducing end reaching the catalytic residues Asp399 and Glu366, which lie on different chains, as indicated. Bridging water molecules are colored purple. Structure 2008 16, 766-775DOI: (10.1016/j.str.2008.01.019) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 7 Sf6 TSPΔN Trimer Surfaces The trimer is (A) oriented to display the solvent-exposed side of one monomer (as in Figure 1) or (B) rotated by 70° about the three-fold axis to permit a view into the cleft between two neighboring subunits (as in Figure 2). Surfaces colored according to the electrostatic potential calculated by the program DELPHI, with deepest shades of blue and red corresponding to potentials of ±10 kT (Rocchia et al., 2001). All mutated acidic residues are labeled. Sf6 TSPΔN (C) or P22 TSPΔN (D) with O-antigen octasaccharides (sticks) bound to the surface (monomers in green, red, and blue). View from the N terminus along the three-fold axes. (A) and (B) were drawn with GRASP (Nicholls et al., 1991), (C) and (D) with PyMOL (DeLano, 2002). Structure 2008 16, 766-775DOI: (10.1016/j.str.2008.01.019) Copyright © 2008 Elsevier Ltd Terms and Conditions