<jats:p>The glycosyltransferase SnogD from <jats:italic>Streptomyces nogalater</jats:italic> transfers a nogalamine moiety to the metabolic intermediate 3′,4′‐demethoxynogalose‐1‐hydroxynogalamycinone during the final steps of biosynthesis of the aromatic polyketide nogalamycin. The crystal structure of recombinant SnogD, as an apo‐enzyme and with a bound nucleotide, 2‐deoxyuridine‐5′‐diphosphate, was determined to 2.6 Å resolution. Reductive methylation of SnogD was crucial for reproducible preparation of diffraction quality crystals due to creation of an additional intermolecular salt bridge between methylated lysine residue Lys384 and Glu374* from an adjacent molecule in the crystal lattice. SnogD is a dimer both in solution and in the crystal, and the enzyme subunit displays a fold characteristic of the GT‐B family of glycosyltransferases. Binding of the nucleotide is associated with rearrangement of two active‐site loops. Site‐directed mutagenesis shows that two active‐site histidine residues, His25 and His301, are critical for the glycosyltransferase activities of SnogD both <jats:italic>in vivo</jats:italic> and <jats:italic>in vitro</jats:italic>. The crystal structures and the functional data are consistent with a role for His301 in binding of the diphosphate group of the sugar donor substrate, and a function of His25 as a catalytic base in the glycosyl transfer reaction.<jats:p><jats:bold>Database</jats:bold> The atomic coordinates and structure factors have been deposited with the RCSB Protein Data Bank under accession numbers <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4AMB">4AMB</jats:ext-link>, <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4AMG">4AMG</jats:ext-link> and <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4AN4">4AN4</jats:ext-link><jats:p><jats:bold>Structured digital abstract</jats:bold><jats:p><jats:list list-type="explicit-label"> <jats:list-item><jats:p> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.uniprot.org/uniprot/Q9RN61">snogD</jats:ext-link><jats:bold> </jats:bold>and <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.uniprot.org/uniprot/Q9RN61">snogD</jats:ext-link><jats:bold> </jats:bold><jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0407">bind</jats:ext-link> by <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0114">x‐ray crystallography</jats:ext-link> (View Interaction: <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-8386021">1</jats:ext-link>, <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-8386048">2</jats:ext-link>)</jats:list-item> </jats:list>