6T8I | pdb_00006t8i

Crystal structure of wild type EndoBT-3987 from Bacteroides thetaiotamicron VPI-5482

• PDB DOI: https://doi.org/10.2210/pdb6T8I/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-24 Released: 2020-02-26 
• Deposition Author(s): Trastoy, B., Du, J.J., Klontz, E.H., Cifuente, J.O., Sundberg, E.J., Guerin, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

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

Trastoy, B., Du, J.J., Klontz, E.H., Li, C., Cifuente, J.O., Wang, L.X., Sundberg, E.J., Guerin, M.E.

(2020) Nat Commun 11: 899-899

• PubMed: 32060313 
• DOI: https://doi.org/10.1038/s41467-020-14754-7
• Primary Citation Related Structures: 
  6T8I, 6T8K, 6T8L, 6TCV, 6TCW


• 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-Man ₉ GlcNAc ₂ Asn substrate complex, and two EndoBT-3987-Man ₉ GlcNAc and EndoBT-3987-Man ₅ GlcNAc 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.

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Organizational Affiliation: 
• Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain. [e-mail].
Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Program in Molecular Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. [e-mail].
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. [e-mail].
Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. [e-mail].
Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA. [e-mail].
Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain. [e-mail].
IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.38 kDa 
• Atom Count: 3,692 
• Modeled Residue Count: 434 
• Deposited Residue Count: 451 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-beta-N-acetylglucosaminidase F1	A	451	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_3987
UniProt
Find proteins for Q8A0N4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A0N4  Go to UniProtKB:  Q8A0N4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.578	α = 90
b = 74.578	β = 90
c = 133.54	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Trastoy, B., Du, J.J., Klontz, E.H., Cifuente, J.O., Sundberg, E.J., Guerin, M.E.

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description