The crystal structure of a cyanogenic β-glucosidase from white clover, a family 1 glycosyl hydrolase  T Barrett, CG Suresh, SP Tolley, EJ Dodson, MA Hughes  Structure  Volume 3, Issue 9, Pages 951-960 (September 1995) DOI: 10.1016/S0969-2126(01)00229-5

Figure 1 The reaction catalyzed by the cyanogenic β-glucosidase from white clover. Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 2 Secondary structure diagram of white clover cyanogenic β-glucosidase showing the eight parallel β strands that form the barrel core. The β strands are represented by rectangles and the α helices by circles. The eight β strands forming the barrel are labelled B1–B8 and the eight peripheral helices A1–A8. Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 3 The overall topology of the cyanogenic β-glucosidase (CBG) molecule. (a) Stereo Cα trace of the CBG monomer. The residues forming the catalytic pocket are also shown. (b) Ribbon diagram showing the overall fold of the molecule. Glu183 is in green and Glu397 in red. (Figure generated using QUANTA [Molecular Simulations Inc., Waltham, MA].). Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 3 The overall topology of the cyanogenic β-glucosidase (CBG) molecule. (a) Stereo Cα trace of the CBG monomer. The residues forming the catalytic pocket are also shown. (b) Ribbon diagram showing the overall fold of the molecule. Glu183 is in green and Glu397 in red. (Figure generated using QUANTA [Molecular Simulations Inc., Waltham, MA].). Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 4 The catalytic region. (a) A stereoview of the active site pocket showing residues Glu183 and Glu397 and their local environments (which are consistent with their respective roles as acid/base catalyst and nucleophile). (b) The same region with 2Fo–Fc density calculated using the current model (the map is contoured at a level of 1σ). Water molecules were omitted for improved clarity. (The figure was generated using O/OPLOT [36].). Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 4 The catalytic region. (a) A stereoview of the active site pocket showing residues Glu183 and Glu397 and their local environments (which are consistent with their respective roles as acid/base catalyst and nucleophile). (b) The same region with 2Fo–Fc density calculated using the current model (the map is contoured at a level of 1σ). Water molecules were omitted for improved clarity. (The figure was generated using O/OPLOT [36].). Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 5 The solvent-accessible surface for the entire molecule, showing the active-site pocket (Glu83 magenta and Glu397 yellow). The probe radius used was 1.4 å. (Figure generated using GRASP [43].). Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 6 The linamarin–CBG complex. A stereoview showing the active-site residues, along with the 3Fo–2Fc density for a disordered glucose residue, contoured at 0.8σ (calculated using data from the linamarin complex with phases derived from the current model). (Figure generated using O/OPLOT [36].). Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 7 The clover CBG dimer and associated interface, viewed approximately perpendicular to the dyad axis. (a) Stereoview of the Cα trace for each of the monomers forming the CBG dimer, together with associated water molecules shown as dots. (b) A stereoview ribbon diagram showing the dimer interface created by the two CBG monomers. It comprises mainly hydrophobic residues and contains only six hydrogen bonds (shown as dotted red lines). (This figure was generated using SETOR [44].). Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 7 The clover CBG dimer and associated interface, viewed approximately perpendicular to the dyad axis. (a) Stereoview of the Cα trace for each of the monomers forming the CBG dimer, together with associated water molecules shown as dots. (b) A stereoview ribbon diagram showing the dimer interface created by the two CBG monomers. It comprises mainly hydrophobic residues and contains only six hydrogen bonds (shown as dotted red lines). (This figure was generated using SETOR [44].). Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)

Figure 8 A Ramachandran plot of the current model. Three residues are located in ‘generously allowed’ regions (denoted by ∼p). These correspond to Trp454, Ala68 and Arg300. Trp454 and Ala68 have well defined density and make favourable hydrogen bonds with water molecules. Arg300 is located on the surface of the molecule, in a short helix, and is disordered from Cγ. All of its main-chain atoms are, however, clearly defined, with the carbonyl oxygen atom hydrogen bonding to both a water molecule and the amide nitrogen of Leu303. This figure was generated using PROCHECK [45]. Structure 1995 3, 951-960DOI: (10.1016/S0969-2126(01)00229-5)