6ZJ6 | pdb_00006zj6

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with cyclohexylmethyl-Glc-1,3-isofagomine

• PDB DOI: https://doi.org/10.2210/pdb6ZJ6/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides xylanisolvens XB1A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-06-27 Released: 2020-11-18 
• Deposition Author(s): Thompson, A.J., Sobala, L.F., Fernandes, P.Z., Hakki, Z., Howe, J.D., Hill, M., Zitzmann, N., Davies, S., Stamataki, Z., Butters, T.D., Alonzi, D.S., Williams, S.J., Davies, G.J.
• Funding Organization(s): European Research Council (ERC), Australian Research Council (ARC), Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.09 Å
• R-Value Free: 
  0.136 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.113 (Depositor), 0.113 (DCC) 

Starting Model: experimental

Literature

Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.

Sobala, L.F., Fernandes, P.Z., Hakki, Z., Thompson, A.J., Howe, J.D., Hill, M., Zitzmann, N., Davies, S., Stamataki, Z., Butters, T.D., Alonzi, D.S., Williams, S.J., Davies, G.J.

(2020) Proc Natl Acad Sci U S A 117: 29595-29601

• PubMed: 33154157 
• DOI: https://doi.org/10.1073/pnas.2013620117
• Primary Citation Related Structures: 
  6ZDC, 6ZDF, 6ZDK, 6ZDL, 6ZFA, 6ZFN, 6ZFQ, 6ZJ1, 6ZJ5, 6ZJ6


• PubMed Abstract: 
  

  Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition, and function. N-linked glycans are synthesized from Glc ₃ Man ₉ GlcNAc ₂ precursors that are trimmed and modified in the endoplasmic reticulum (ER) and Golgi apparatus by glycoside hydrolases and glycosyltransferases. Endo-α-1,2-mannosidase (MANEA) is the sole endo -acting glycoside hydrolase involved in N-glycan trimming and is located within the Golgi, where it allows ER-escaped glycoproteins to bypass the classical N-glycosylation trimming pathway involving ER glucosidases I and II. There is considerable interest in the use of small molecules that disrupt N-linked glycosylation as therapeutic agents for diseases such as cancer and viral infection. Here we report the structure of the catalytic domain of human MANEA and complexes with substrate-derived inhibitors, which provide insight into dynamic loop movements that occur on substrate binding. We reveal structural features of the human enzyme that explain its substrate preference and the mechanistic basis for catalysis. These structures have inspired the development of new inhibitors that disrupt host protein N-glycan processing of viral glycans and reduce the infectivity of bovine viral diarrhea and dengue viruses in cellular models. These results may contribute to efforts aimed at developing broad-spectrum antiviral agents and help provide a more in-depth understanding of the biology of mammalian glycosylation.

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Organizational Affiliation: 
• Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia.
Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, United Kingdom.
School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia; [e-mail] [e-mail].
Department of Chemistry, University of York, York YO10 5DD, United Kingdom; [e-mail] [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: 44.67 kDa 
• Atom Count: 3,698 
• Modeled Residue Count: 360 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 71	A [auth AAA]	385	Bacteroides xylanisolvens XB1A	Mutation(s): 0  Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A) Explore D6D1V7  Go to UniProtKB:  D6D1V7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC (Subject of Investigation/LOI)	I [auth AAA]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
IFM (Subject of Investigation/LOI)	H [auth AAA]	5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE C6 H13 N O3 QPYJXFZUIJOGNX-HSUXUTPPSA-N
QTE (Subject of Investigation/LOI)	G [auth AAA]	methylcyclohexane C7 H14 UAEPNZWRGJTJPN-UHFFFAOYSA-N
EDO	B [auth AAA], C [auth AAA], D [auth AAA], E [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	F [auth AAA]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.09 Å
• R-Value Free:  0.136 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.113 (Depositor), 0.113 (DCC) 

Diffraction Data: https://doi.org/10.5281/zenodo.4288341

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.981	α = 90
b = 107.981	β = 90
c = 67.282	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Thompson, A.J., Sobala, L.F., Fernandes, P.Z., Hakki, Z., Howe, J.D., Hill, M., Zitzmann, N., Davies, S., Stamataki, Z., Butters, T.D., Alonzi, D.S., Williams, S.J., Davies, G.J.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	322942
Australian Research Council (ARC)	Australia	DP120101396
Australian Research Council (ARC)	Australia	FT130100103
Australian Research Council (ARC)	Australia	DP180101957
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/G016127/1

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 2.0: 2021-01-20
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description