6T8K

Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with Man9GlcNAc product in P1

Summary for 6T8K

• Entry DOI: 10.2210/pdb6t8k/pdb
• Descriptor: Endo-beta-N-acetylglucosaminidase F1, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: endo-b-n-acetylglucosaminidase, endobt, glycoside hydrolase, hydrolase
• Biological source: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
• Total number of polymer chains: 2
• Total formula weight: 101828.60

Authors

Trastoy, B.,Du, J.J.,Klontz, E.H.,Cifuente, J.O.,Sundberg, E.J.,Guerin, M.E. (deposition date: 2019-10-24, release date: 2020-02-26, Last modification date: 2024-01-24)

Primary citation

Trastoy, B.,Du, J.J.,Klontz, E.H.,Li, C.,Cifuente, J.O.,Wang, L.X.,Sundberg, E.J.,Guerin, M.E.
Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides.
Nat Commun, 11:899-899, 2020

PubMed Abstract: The human gut microbiota plays a central role not only in regulating the metabolism of nutrients but also promoting immune homeostasis, immune responses and protection against pathogen colonization. The genome of the Gram-negative symbiont Bacteroides thetaiotaomicron, a dominant member of the human intestinal microbiota, encodes polysaccharide utilization loci PULs, the apparatus required to orchestrate the degradation of a specific glycan. EndoBT-3987 is a key endo-β-N-acetylglucosaminidase (ENGase) that initiates the degradation/processing of mammalian high-mannose-type (HM-type) N-glycans in the intestine. Here, we provide structural snapshots of EndoBT-3987, including the unliganded form, the EndoBT-3987-ManGlcNAcAsn substrate complex, and two EndoBT-3987-ManGlcNAc and EndoBT-3987-ManGlcNAc product complexes. In combination with alanine scanning mutagenesis and activity measurements we unveil the molecular mechanism of HM-type recognition and specificity for EndoBT-3987 and an important group of the GH18 ENGases, including EndoH, an enzyme extensively used in biotechnology, and for which the mechanism of substrate recognition was largely unknown.

PubMed: 32060313
DOI: 10.1038/s41467-020-14754-7

Experimental method

X-RAY DIFFRACTION (2 Å)