6ZJ5

Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcDMJ and hexatungstotellurate(VI) TEW


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.188 

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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
Glycoprotein endo-alpha-1,2-mannosidaseA [auth AAA]382Homo sapiensMutation(s): 0 
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
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEW
Query on TEW

Download Ideal Coordinates CCD File 
F [auth AAA],
G [auth AAA],
H [auth AAA]
6-tungstotellurate(VI)
O24 Te W6
JDLYBIMRCSJRQJ-UHFFFAOYSA-M
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
B [auth AAA],
C [auth AAA],
D [auth AAA]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
GLC (Subject of Investigation/LOI)
Query on GLC

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

Download Ideal Coordinates CCD File 
I [auth AAA]1-DEOXYMANNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-KVTDHHQDSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth AAA]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.549α = 90
b = 128.549β = 90
c = 48.264γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata 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

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 2.0: 2021-01-20
    Changes: Atomic model, Data collection, Database references, Derived calculations