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. 2007 Sep;19(9):2886–2897. doi: 10.1105/tpc.106.045682

Figure 5.

Figure 5.

Comparison of the Region around Trp-388 with Respect to Bacteria, Archaea, and Higher Plants.

(A) The three different conformations of Trp-388 in 16 β-glycosidases from bacteria (blue), archaea (brown), higher plants (red), and SG from Rauvolfia (green) described in this study. The location of the sugar binding site compared with the Trp side chains and direction to the enzyme surface are indicated by black arrows. Gly-386 and Gly-387 are labeled to indicate the direction to the N terminus, and the distance between Cα of Trp-388 in microbial and eukaryotic enzymes is illustrated by a yellow arrow. The sequence numbering is according to SG. The structures shown are as follows: 1NP2, β-glycosidase from Thermus nonproteolyticus HG102; 1UG6, β-glycosidase (TTHB087) from Thermus thermophilus HB8; 1GNX, β-glucosidase (Bgl3) from Streptomyces sp QM-B814; 1OD0, β-glucosidase A (BglA) from Thermotoga maritima MSB8; 1QOX, β-glucosidase (BglA) from Bacillus circulans subsp Alkalophilus; 1E4I, β-glucosidase A (BglA) from Paenibacillus polymyxa; 1CBG, cyanogenic β-glucosidase from T. repens; SG, strictosidine glucosidase from R. serpentina; 1E1E, Zm Glu1 from Z. mays; 1HXJ, Zmp60.1 from Z. mays; 1V02, Dhurrinase1 from S. bicolor; 2DGA, Ta Glu1b from T. aestivum; 1PBG, 6-P-β-galactosidase from Lactococcus lactis Z268; 1VFF, alkyl β-glycosidase (BGPh; PH0366) from Pyrococcus horikoshii OT3; 1GOW, β-glycosidase S (LacS;S-β-gly; SSO3019) from Sulfolobus solfataricus P2; 1QVB, β-glycosidase from Thermosphaera aggregans M11TL.

(B) To illustrate the different backbone orientations of the glycosidases, (A) was rotated by 90° around the x axis (colors are as in [A]). Near Thr-372 (yellow arrow), all the main chains diverge in three groups depending on their origin (bacteria, achaea, and higher plants). Archaea and bacteria backbones merge around residue Ala-383 (yellow arrow). Microbial and plant main chains merge after Trp-388. For better recognition, Gly-387 (yellow arrow) and the substrate binding region are marked. The sequence numbering is according to SG.