Fig. 4: Predicted structure of B. dorei’s GH33 resembles the crystallized GH33 sialidase of B. thetaiotaomicron. | Nature Communications

Fig. 4: Predicted structure of B. dorei’s GH33 resembles the crystallized GH33 sialidase of B. thetaiotaomicron.

From: CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei

Fig. 4: Predicted structure of B. dorei’s GH33 resembles the crystallized GH33 sialidase of B. thetaiotaomicron.The alternative text for this image may have been generated using AI.

A 3D structure of B. dorei’s GH33 sialidase, as predicted by AlphaFold based on the protein sequence, excluding the first 23 residues for which the pLDDT values are low. The active site and carbohydrate-binding site are indicated by a green circle. B Alignment of GH33 protein structures of B. dorei (predicted, blue) and B. thetaiotaomicron VPI 5482 (crystallized, red; PDB code 4BBW). The first 23 residues from B. dorei’s enzyme were excluded similarly to (A). C The wide-open substrate-binding groove of the active site in B. dorei (left) and B. thetaiotaomicron VPI 5482 (right). Residues essential for activity are highlighted in red and residues responsible for laying out the wide-open groove are highlighted in magenta. Of the latter group of residues, although one of the three is not conserved between B. dorei and B. thetaiotaomicron (Ala228 and Val228, respectively), the wide topology of the groove is preserved.

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