4AMB

Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater

Summary for 4AMB

• Entry DOI: 10.2210/pdb4amb/pdb
• Descriptor: SNOGD, DEOXYURIDINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: transferase, polyketide biosynthesis, gt1 family, nogalamycin
• Biological source: STREPTOMYCES NOGALATER
• Total number of polymer chains: 2
• Total formula weight: 84281.29

Authors

Claesson, M.,Siitonen, V.,Dobritzsch, D.,Metsa-Ketela, M.,Schneider, G. (deposition date: 2012-03-08, release date: 2012-09-05, Last modification date: 2023-12-20)

Primary citation

Claesson, M.,Siitonen, V.,Dobritzsch, D.,Metsa-Ketela, M.,Schneider, G.
Crystal Structure of the Glycosyltransferase Snogd from the Biosynthetic Pathway of the Nogalamycin in Streptomyces Nogalater.
FEBS J., 279:3251-, 2012

PubMed Abstract: The glycosyltransferase SnogD from Streptomyces nogalater 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 in vivo and in vitro. 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.

PubMed: 22804797
DOI: 10.1111/J.1742-4658.2012.08711.X

Experimental method

X-RAY DIFFRACTION (2.62 Å)