6T8L
Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 with Man9GlcNAc product in P212121
Summary for 6T8L
| Entry DOI | 10.2210/pdb6t8l/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 VPI-5482 |
| Total number of polymer chains | 1 |
| Total formula weight | 50914.30 |
| 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 Cited by 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: 32060313DOI: 10.1038/s41467-020-14754-7 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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