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. 2009 Mar 19;28(7):959–968. doi: 10.1038/emboj.2009.40

Figure 2.

Figure 2

Structural features of the ‘dynamic catalytic loop'. (A, B) A reversible disulphide bond formation. A disulphide bond formation in the oxidized form (A), and a breakage of the disulphide bond in the reduced form (B) of human SSADH are shown as a stick model, and their omit electron densities (blue mesh) are contoured at 3.0σ. (C) Structural changes of the ‘dynamic catalytic loop'. The catalytic loops of the oxidized and reduced forms of the wild-type SSADH (coloured salmon and cyan, respectively) are superimposed. The disulphide bond in the oxidized form, and the two cysteine residues in the reduced form of the SSADH are shown as a stick model and labelled appropriately. The R334 (involved in the substrate binding) and the E306 (functions as a general base) residues of the oxidized and reduced forms of SSADH are presented as stick models. (D, E) Blocking of the SSA-binding tunnel (D) and the nicotinamide ring-binding tunnel (E) by the ‘dynamic catalytic loop' in the oxidized form. The oxidized (ribbon model, coloured salmon) and reduced (surface model, coloured grey) forms of SSADH were superimposed, The SSA and nicotinamide ring-binding tunnels are indicated. The V341 residue that blocks the nicotinamide ring-binding tunnel is shown as a stick model and labelled. (F) Stabilization of the ‘dynamic catalytic loop' in the oxidized ‘closed' form. The ‘dynamic catalytic loop' in the oxidized form is presented in salmon colour, and the residues involved in the hydrogen bonding are as stick model. (G) Stabilization of the ‘dynamic catalytic loop' in the reduced ‘open' form. The ‘dynamic catalytic loop' in the reduced form is presented in cyan colour in the same view with that of in the oxidized form, and the residues involved in the hydrogen bonding are as stick model. For both (F, G), the neighbouring residues involved in the hydrogen bonding with the ‘dynamic catalytic loop' are shown as a stick model in grey colour, and water molecules involved in the stabilization of the loop are presented as red spheres. The hydrogen bond interactions are indicated by black dotted lines.