Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides

Beatriz Trastoy (), Jonathan J. Du, Erik H. Klontz, Chao Li, Javier O. Cifuente, Lai-Xi Wang, Eric J. Sundberg () and Marcelo E. Guerin ()
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Beatriz Trastoy: Bizkaia Technology Park
Jonathan J. Du: University of Maryland School of Medicine
Erik H. Klontz: University of Maryland School of Medicine
Chao Li: University of Maryland
Javier O. Cifuente: Bizkaia Technology Park
Lai-Xi Wang: University of Maryland
Eric J. Sundberg: University of Maryland School of Medicine
Marcelo E. Guerin: Bizkaia Technology Park

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: 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-Man9GlcNAc2Asn substrate complex, and two EndoBT-3987-Man9GlcNAc and EndoBT-3987-Man5GlcNAc 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.

Date: 2020
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DOI: 10.1038/s41467-020-14754-7

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