4AD3

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with Glucose-1,3-deoxymannojirimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GLCClick on this verticalbar to view detailsBest fitted DMJClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Structural and Mechanistic Insight Into N-Glycan Processing by Endo-Alpha-Mannosidase.

Thompson, A.J.Williams, R.J.Hakki, Z.Alonzi, D.S.Wennekes, T.Gloster, T.M.Songsrirote, K.Thomas-Oates, J.E.Wrodnigg, T.M.Spreitz, J.Stutz, A.E.Butters, T.D.Williams, S.J.Davies, G.J.

(2012) Proc Natl Acad Sci U S A 109: 781

  • DOI: https://doi.org/10.1073/pnas.1111482109
  • Primary Citation of Related Structures:  
    4ACY, 4ACZ, 4AD0, 4AD1, 4AD2, 4AD3, 4AD4, 4AD5

  • PubMed Abstract: 

    N-linked glycans play key roles in protein folding, stability, and function. Biosynthetic modification of N-linked glycans, within the endoplasmic reticulum, features sequential trimming and readornment steps. One unusual enzyme, endo-α-mannosidase, cleaves mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. Here, using two bacterial orthologs, we present the first structural and mechanistic dissection of endo-α-mannosidase. Structures solved at resolutions 1.7-2.1 Å reveal a (β/α)(8) barrel fold in which the catalytic center is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain. Enzymatic cleavage of authentic Glc(1/3)Man(9)GlcNAc(2) yields Glc(1/3)-Man. Using the bespoke substrate α-Glc-1,3-α-Man fluoride, the enzyme was shown to act with retention of anomeric configuration. Complexes with the established endo-α-mannosidase inhibitor α-Glc-1,3-deoxymannonojirimycin and a newly developed inhibitor, α-Glc-1,3-isofagomine, and with the reducing-end product α-1,2-mannobiose structurally define the -2 to +2 subsites of the enzyme. These structural and mechanistic data provide a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.


  • Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCOSYL HYDROLASE FAMILY 71
A, B, C, D
380Bacteroides xylanisolvens XB1AMutation(s): 0 
EC: 3.2.1.130
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
DMJ
Query on DMJ

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
1-DEOXYMANNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-KVTDHHQDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.478α = 90
b = 222.478β = 90
c = 84.715γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GLCClick on this verticalbar to view detailsBest fitted DMJClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Other
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary