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![[Figure 3]](rr5209fig3mag.jpg)
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Figure 3
Structure of the β-galactosidase BbgIII from B. bifidum strain NCIMB41171: domain scheme, overall structure, difference between chains A and B, and active site. (a) The domains of BbgIII; those in the present structure are indicated above the scheme and by numbers under the scheme. 1, 30–181, GH2-associated, Ig-like; 2, 182–302, GH2-associated, Ig-like; 3, 303–643, GH2, catalytic (βα)8 `TIM barrel'; 4, 644–764, GH2-associated, Ig-like; 5, 765–878, GH2-associated, Ig-like; 6, 886–959 and N-terminal 9–22, Big_4 (referred to in the text as Big_4-1); 7, 962–1038 and a region after the next domain, 1214–1286, Big_4 (Big_4-2); 8, 1044–1210, CBM32 (there are two CBM32 domains in the full-length sequence, but only the first CBM32 domain is in our construct, so we call it just CBM32 throughout this paper). (b) The fold of chain A with the domains coloured as in (a) and shown in ribbon representation. The binding site is indicated by the catalytic residues Glu533 (nucleophile) and Glu447 (catalytic acid), which are shown as spheres. (c) Superposition of chain B on chain A. The core domains 1–5 superpose very well (ice blue for chain A, lighter grey for chain B), while domains 6–8 (brown for A, green for B) differ completely in the way they wrap around the core domains. The active site is indicated by a glycerol molecule (shown as spheres). While the active site is easily accessed in chain B, the entrance in chain A is partially blocked by the CBM32 domain. (d) Close-up of the active site. Superposition of PDB entry 4cuc (in complex with LacNAc) on BbgIII. The catalytic residues as well as other residues that line the binding site in PDB entry 4cuc superpose well on BbgIII, with a glycerol molecule in a location close to LacNAc in PDB entry 4cuc. The binding-site residues from PDB entry 4cuc are shown in parentheses. The figure shows how the CBM32 domain in chain A would clash with lactose, with the loop around Ala1111 occupying the position of the second half of the ligand, close to Trp568. The binding-site residues of BbgIII are in dark green, glycerol is in magenta, the residues of PDB entry 4cuc are in yellow and CBM32 is in ice blue. Figs. 3 ![[link]](../../../../../../logos/arrows/d_arr.gif) , 4, 6 and 7 were prepared using CCP4mg (McNicholas et al., 2011). |
![[Figure 3]](rr5209fig3.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
