7NWF

Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with hybrid-type glycan (GalGlcNAcMan5GlcNAc) product

Summary for 7NWF

• Entry DOI: 10.2210/pdb7nwf/pdb
• Descriptor: Endo-beta-N-acetylglucosaminidase F1, beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... (4 entities in total)
• Functional Keywords: endo-b-n-acetylglucosaminidase, endobt-3987, bt3987, glycoside hydrolase, hydrolase
• Biological source: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
• Total number of polymer chains: 1
• Total formula weight: 50775.18

Authors

Trastoy, B.,Du, J.J.,Garcia-Alija, M.,Sundberg, E.J.,Guerin, M.E. (deposition date: 2021-03-16, release date: 2021-08-04, Last modification date: 2024-01-31)

Primary citation

Trastoy, B.,Du, J.J.,Li, C.,Garcia-Alija, M.,Klontz, E.H.,Roberts, B.R.,Donahue, T.C.,Wang, L.X.,Sundberg, E.J.,Guerin, M.E.
GH18 endo-beta-N-acetylglucosaminidases use distinct mechanisms to process hybrid-type N-linked glycans.
J.Biol.Chem., 297:101011-101011, 2021

PubMed Abstract: N-glycosylation is one of the most abundant posttranslational modifications of proteins, essential for many physiological processes, including protein folding, protein stability, oligomerization and aggregation, and molecular recognition events. Defects in the N-glycosylation pathway cause diseases that are classified as congenital disorders of glycosylation. The ability to manipulate protein N-glycosylation is critical not only to our fundamental understanding of biology but also for the development of new drugs for a wide range of human diseases. Chemoenzymatic synthesis using engineered endo-β-N-acetylglucosaminidases (ENGases) has been used extensively to modulate the chemistry of N-glycosylated proteins. However, defining the molecular mechanisms by which ENGases specifically recognize and process N-glycans remains a major challenge. Here we present the X-ray crystal structure of the ENGase EndoBT-3987 from Bacteroides thetaiotaomicron in complex with a hybrid-type glycan product. In combination with alanine scanning mutagenesis, molecular docking calculations and enzymatic activity measurements conducted on a chemically engineered monoclonal antibody substrate unveil two mechanisms for hybrid-type recognition and processing by paradigmatic ENGases. Altogether, the experimental data provide pivotal insight into the molecular mechanism of substrate recognition and specificity for GH18 ENGases and further advance our understanding of chemoenzymatic synthesis and remodeling of homogeneous N-glycan glycoproteins.

PubMed: 34324829
DOI: 10.1016/j.jbc.2021.101011

Experimental method

X-RAY DIFFRACTION (2 Å)