Koshland, D. E. Stereochemistry and the mechanism of enzymatic reactions. Biol. Rev. 28, 416–436 (1953).
Nasseri, S. A., Betschart, L., Opaleva, D., Rahfeld, P. & Withers, S. G. A mechanism-based approach to screening metagenomic libraries for discovery of unconventional glycosidases. Angew. Chem. 130, 11529–11534 (2018).
Wolfenden, R., Lu, X. & Young, G. Spontaneous hydrolysis of glycosides. J. Am. Chem. Soc. 120, 6814–6815 (1998).
Watts, A. G. et al. Trypanosoma cruzi trans-sialidase operates through a covalent sialyl-enzyme intermediate: tyrosine is the catalytic nucleophile. J. Am. Chem. Soc. 125, 7532–7533 (2003).
Vocadlo, D. J. & Withers, S. G. Detailed comparative analysis of the catalytic mechanisms of β-N-acetylglucosaminidases from families 3 and 20 of glycoside hydrolases. Biochemistry 44, 12809–12818 (2005).
Namchuk, M. N. & Withers, S. G. Mechanism of Agrobacterium β-glucosidase: kinetic analysis of the role of noncovalent enzyme/substrate interactions. Biochemistry 34, 16194–16202 (1995).
Mistry, J. et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).
Drula, E. et al. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 50, D571–D577 (2022).
Yip, V. L. Y. & Withers, S. G. Family 4 glycosidases carry out efficient hydrolysis of thioglycosides by an α,β-elimination mechanism. Angew. Chem. Int. Ed. 45, 6179–6182 (2006).
Jongkees, S. A. K. & Withers, S. G. Glycoside cleavage by a new mechanism in unsaturated glucuronyl hydrolases. J. Am. Chem. Soc. 133, 19334–19337 (2011).
Rahfeld, P. et al. An enzymatic pathway in the human gut microbiome that converts A to universal O type blood. Nat. Microbiol. 4, 1475–1485 (2019).
Lorenz, P. & Eck, J. Metagenomics and industrial applications. Nat. Rev. Microbiol. 3, 510–516 (2005).
Viborg, A. H. et al. A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). J. Biol. Chem. 294, 15973–15986 (2019).
Hallgren, J. et al. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. Preprint at bioRxiv https://doi.org/10.1101/2022.04.08.487609 (2022).
Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat. Biotechnol. 40, 1023–1025 (2022).
Liou, C. S. et al. A metabolic pathway for activation of dietary glucosinolates by a human gut symbiont. Cell 180, 717–728 (2020).
Ravcheev, D. A., Godzik, A., Osterman, A. L. & Rodionov, D. A. Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks. BMC Genomics 14, 873 (2013).
Liu, H. et al. Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. Cell Rep. 34, 108789 (2021).
Yip, V. L. Y. et al. An unusual mechanism of glycoside hydrolysis involving redox and elimination steps by a family 4 β-glycosidase from Thermotoga maritima. J. Am. Chem. Soc. 126, 8354–8355 (2004).
Jäger, M., Hartmann, M., de Vries, J. G. & Minnaard, A. J. Catalytic regioselective oxidation of glycosides. Angew. Chemie Int. Ed. 52, 7809–7812 (2013).
Morris, P. E., Hope, K. D. & Kiely, D. E. The isomeric composition of d-ribo-hexos-3-ulose (3-keto-d-glucose) in aqueous solution. J. Carbohydr. Chem. 8, 515–530 (1989).
Allouch, J. et al. The three-dimensional structures of two β-agarases. J. Biol. Chem. 278, 47171–47180 (2003).
Lemke, A., Kiderlen, A. F. & Kayser, O. Amphotericin B. Appl. Microbiol. Biotechnol. 68, 151–162 (2005).
Arsic, B. et al. 16-membered macrolide antibiotics: a review. Int. J. Antimicrob. Agents 51, 283–298 (2018).
Zhao, Q. et al. Neriifolin from seeds of Cerbera manghas L. induces cell cycle arrest and apoptosis in human hepatocellular carcinoma HepG2 cells. Fitoterapia 82, 735–741 (2011).
Sugawara, K. et al. Elsamicins A and B, new antitumor antibiotics related to chartreusin. 2. Structures of elsamicins A and B. J. Org. Chem. 52, 996–1001 (1987).
Martens, E. C. et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9, e1001221 (2011).
van Beeumen, J. & de Ley, J. Hexopyranoside: cytochrome c oxidoreductase from Agrobacterium tumefaciens. Eur. J. Biochem. 6, 331–343 (1968).
Takeuchi, M., Asano, N., Kameda, Y. & Matsui, K. Physiological role of glucoside 3-dehydrogenase and cytochrome c551 in the sugar oxidizing system of Flavobacterium saccharophilum. J. Biochem. 103, 938–943 (1988).
Bernaerts, M. J. & De Ley, J. Microbiological formation and preparation of 3-ketoglycosides from disaccharides. J. Gen. Microbiol. 22, 129–136 (1960).
Grebner, E. E. & Feingold, D. S. d-Aldohexopyranoside dehydrogenase of Agrobacterium tumefaciens. Biochem. Biophys. Res. Commun. 19, 37–42 (1965).
Hayano, K. & Fukui, S. Purification and properties of 3-ketosucrose-forming enzyme from the cells of Agrobacterium tumefaciens. J. Biol. Chem. 242, 3655–3672 (1967).
Kuritani, Y. et al. Conversion of levoglucosan into glucose by the coordination of four enzymes through oxidation, elimination, hydration, and reduction. Sci. Rep. 10, 20066 (2020).
Kaur, A. et al. Identification of levoglucosan degradation pathways in bacteria and sequence similarity network analysis. Arch. Microbiol. 205, 155 (2023).
Braune, A., Engst, W. & Blaut, M. Identification and functional expression of genes encoding flavonoid O– and C-glycosidases in intestinal bacteria. Environ. Microbiol. 18, 2117–2129 (2016).
He, P. et al. Structural mechanism of a dual-functional enzyme DgpA/B/C as both a C-glycoside cleaving enzyme and an O– to C-glycoside isomerase. Acta Pharm. Sin. B 13, 246–255 (2023).
Mori, T. et al. C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. Nat. Commun. 12, 6294 (2021).
Zheng, S. et al. A newly isolated human intestinal bacterium strain capable of deglycosylating flavone C-glycosides and its functional properties. Microb. Cell Fact. 18, 94 (2019).
Taborda, A. et al. Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms. Nat. Commun. 14, 7289 (2023).
Liu, Q. P. et al. Bacterial glycosidases for the production of universal red blood cells. Nat. Biotechnol. 25, 454–464 (2007).
Bell, A. et al. Uncovering a novel molecular mechanism for scavenging sialic acids in bacteria. J. Biol. Chem. 295, 13724–13736 (2020).
Kaur, A. et al. Widespread family of NAD-dependent sulfoquinovosidases at the gateway to sulfoquinovose catabolism. J. Am. Chem. Soc. 145, 28216–28223 (2023).
Bitter, J. et al. Enzymatic β-elimination in natural product O– and C-glycoside deglycosylation. Nat. Commun. 14, 7123 (2023).
Armstrong, Z., Rahfeld, P. & Withers, S. G. Discovery of new glycosidases from metagenomic libraries. Methods Enzymol. 597, 3–23 (2017).
Chen, H.-M. et al. Synthesis and evaluation of sensitive coumarin-based fluorogenic substrates for discovery of α-N-acetyl galactosaminidases through droplet-based screening. Org. Biomol. Chem. 19, 789–793 (2021).
Klock, H. E., Koesema, E. J., Knuth, M. W. & Lesley, S. A. Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins Struct. Funct. Genet. 71, 982–994 (2008).
Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).
Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005).
Barnhart, J. L. & Berk, R. N. Influence of paramagnetic ions and pH on proton NMR relaxation of biologic fluids. Invest. Radiol. 21, 132–136 (1986).
Winter, G. xia2: an expert system for macromolecular crystallography data reduction. J. Appl. Crystallogr. 43, 186–190 (2010).
Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013).
Agirre, J. et al. The CCP4 suite: integrative software for macromolecular crystallography. Acta Crystallogr. D 79, 449–461 (2023).
Tickle, I. J. et al. STARANISO (Global Phasing Ltd, 2018).
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011).
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Agirre, J. et al. Privateer: software for the conformational validation of carbohydrate structures. Nat. Struct. Mol. Biol. 22, 833–834 (2015).
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).
Landau, M. et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 33, W299–W302 (2005).
Gucwa, M. et al. CMM—an enhanced platform for interactive validation of metal binding sites. Protein Sci. 32, e4525 (2023).
Sonnenburg, E. D. et al. Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 141, 1241–1252 (2010).