1FO2

CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA1,2-MANNOSIDASE IN COMPLEX WITH 1-DEOXYMANNOJIRIMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis for catalysis and inhibition of N-glycan processing class I alpha 1,2-mannosidases.

Vallee, F.Karaveg, K.Herscovics, A.Moremen, K.W.Howell, P.L.

(2000) J Biol Chem 275: 41287-41298

  • DOI: https://doi.org/10.1074/jbc.M006927200
  • Primary Citation of Related Structures:  
    1FMI, 1FO2, 1FO3

  • PubMed Abstract: 

    Endoplasmic reticulum (ER) class I alpha1,2-mannosidase (also known as ER alpha-mannosidase I) is a critical enzyme in the maturation of N-linked oligosaccharides and ER-associated degradation. Trimming of a single mannose residue acts as a signal to target misfolded glycoproteins for degradation by the proteasome. Crystal structures of the catalytic domain of human ER class I alpha1,2-mannosidase have been determined both in the presence and absence of the potent inhibitors kifunensine and 1-deoxymannojirimycin. Both inhibitors bind to the protein at the bottom of the active-site cavity, with the essential calcium ion coordinating the O-2' and O-3' hydroxyls and stabilizing the six-membered rings of both inhibitors in a (1)C(4) conformation. This is the first direct evidence of the role of the calcium ion. The lack of major conformational changes upon inhibitor binding and structural comparisons with the yeast alpha1, 2-mannosidase enzyme-product complex suggest that this class of inverting enzymes has a novel catalytic mechanism. The structures also provide insight into the specificity of this class of enzymes and provide a blueprint for the future design of novel inhibitors that prevent degradation of misfolded proteins in genetic diseases.


  • Organizational Affiliation

    Program in Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA1,2-MANNOSIDASE460Homo sapiensMutation(s): 0 
EC: 3.2.1.24 (PDB Primary Data), 3.2.1.113 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKM7 (Homo sapiens)
Explore Q9UKM7 
Go to UniProtKB:  Q9UKM7
PHAROS:  Q9UKM7
GTEx:  ENSG00000177239 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKM7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.174α = 90
b = 96.174β = 90
c = 137.118γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

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 DMJClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary