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Shiga toxin-encoding bacteriophages transfer Shiga toxin genes to Escherichia coli and are responsible for the emergence of pathogenic bacterial strains that cause severe foodborne human diseases. Gene vb_24B_21 is the most highly conserved gene across sequenced Shiga bacteriophages. Protein vb_24B_21 (also termed 933Wp42 and NanS-p) is a carbohydrate esterase with homology to the E. coli chromosomally encoded NanS that deacetylates sialic acid in the intestinal mucus. To assist the functional characterization of vb_24B_21, we have studied its molecular structure by homology modelling its esterase domain and by elucidating the crystal structure of its uncharacterized C-terminal domain at the atomic resolution of 0.97 Å. Our modelling confirms that NanS from the E. coli host is the closest structurally characterized homolog to the esterase domain of vb_24B_21. Like NanS, vb_24B_21 has an atypical active site, comprising a simple catalytic dyad Ser-His and a divergent oxyanion hole. The crystal structure of the C-terminal domain reveals a lectin-like, jelly-roll β-sandwich fold. The domain displays a prominent cleft that bioinformatics analysis predicts to be a carbohydrate binding site without catalytic properties. In summary, our study indicates that vb_24B_21 is a NanS-like atypical esterase that is assisted by a carbohydrate-binding module of yet undetermined binding specificity., (Crown Copyright © 2020. Published by Elsevier Inc. All rights reserved.)