6ZFN

Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with 1-methyl alpha-1,2-mannobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.106 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
Glycoprotein endo-alpha-1,2-mannosidaseA [auth AAA]382Homo sapiensMutation(s): 1 
Gene Names: MANEA
EC: 3.2.1.130
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SRI9 (Homo sapiens)
Explore Q5SRI9 
Go to UniProtKB:  Q5SRI9
PHAROS:  Q5SRI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SRI9
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-methyl alpha-D-mannopyranosideB [auth A]2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G49351KY
GlyCosmos:  G49351KY
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth AAA]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.752α = 90
b = 81.68β = 92.934
c = 52.994γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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

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 1.2: 2021-01-20
    Changes: Database references