6ZJ6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.113 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


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

  • DOI: 10.1073/pnas.2013620117
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of York, York YO10 5DD, United Kingdom; sjwill@unimelb.edu.au gideon.davies@york.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl hydrolase family 71A [auth AAA]385Bacteroides xylanisolvens XB1AMutation(s): 0 
Gene Names: BXY_34140
UniProt
Find proteins for D6D1V7 (Bacteroides xylanisolvens XB1A)
Explore D6D1V7 
Go to UniProtKB:  D6D1V7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6D1V7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
I [auth AAA]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
IFM (Subject of Investigation/LOI)
Query on IFM

Download Ideal Coordinates CCD File 
H [auth AAA]5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
 Ligand Interaction
QTE (Subject of Investigation/LOI)
Query on QTE

Download Ideal Coordinates CCD File 
G [auth AAA]methylcyclohexane
C7 H14
UAEPNZWRGJTJPN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth AAA],
C [auth AAA],
D [auth AAA],
E [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth AAA]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.981α = 90
b = 107.981β = 90
c = 67.282γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United Kingdom322942
Australian Research Council (ARC)AustraliaDP120101396
Australian Research Council (ARC)AustraliaFT130100103
Australian Research Council (ARC)AustraliaDP180101957
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/G016127/1

Revision History  (Full details and data files)

  • 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