Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage Φ24_B

Area of Science:

• Microbiology
• Structural Biology
• Biochemistry

Background:

• Shiga toxin-encoding bacteriophages contribute to pathogenic *Escherichia coli* strains causing severe foodborne illnesses.
• Gene vb_24B_21 is highly conserved among Shiga bacteriophages and encodes a protein with homology to *E. coli* NanS.
• Protein vb_24B_21 is a carbohydrate esterase involved in deacetylating sialic acid in the intestinal mucus.

Purpose of the Study:

• To functionally characterize the vb_24B_21 protein from Shiga bacteriophages.
• To elucidate the molecular structure of the esterase and C-terminal domains of vb_24B_21.
• To understand the structural basis of vb_24B_21's enzymatic activity and potential carbohydrate binding.

Main Methods:

• Homology modeling of the esterase domain of vb_24B_21.
• Crystal structure determination of the C-terminal domain of vb_24B_21 at 0.97 Å resolution.
• Bioinformatics analysis to predict carbohydrate binding sites.

Main Results:

• The esterase domain of vb_24B_21 is structurally similar to *E. coli* NanS, featuring an atypical catalytic dyad (Ser-His) and a divergent oxyanion hole.
• The C-terminal domain adopts a lectin-like, jelly-roll β-sandwich fold.
• A cleft in the C-terminal domain is predicted to be a carbohydrate binding site, lacking catalytic activity.

Conclusions:

• Protein vb_24B_21 functions as a NanS-like atypical esterase.
• vb_24B_21 possesses a distinct carbohydrate-binding module that may influence its function.
• This study provides atomic-level structural insights into a key protein involved in Shiga bacteriophage biology and pathogenicity.