Golgi alpha-mannosidase II in complex with kifunensine

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 

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This is version 1.4 of the entry. See complete history


Comparison of Kifunensine and 1-Deoxymannojirimycin Binding to Class I and II alpha-Mannosidases Demonstrates Different Saccharide Distortions in Inverting and Retaining Catalytic Mechanisms

Shah, N.Kuntz, D.A.Rose, D.R.

(2003) Biochemistry 42: 13812-13816

  • DOI: https://doi.org/10.1021/bi034742r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Mannosidases are key enzymes in the eukaryotic N-glycosylation pathway. These enzymes fall into two broad classes (I and II) and are characteristically different in catalytic mechanism, sequence, and structure. Kifunensine is an alkaloid that is a strong inhibitor against class I alpha-mannosidases but is only a weak inhibitor against class II alpha-mannosidases. In this paper, the 1.80 A resolution crystal structure of kifunensine bound to Drosophila melanogaster Golgi alpha-mannosidase II (dGMII) is presented. Kifunensine adopts a (1,4)B boat conformation in the class II dGMII, which contrasts the (1)C(4) chair conformation seen in class I human endoplasmic reticulum alpha1,2 mannosidase (hERMI, PDB ). The observed conformations are higher in conformational energy than the global minimum (4)C(1) conformation, although the conformation in hERMI is closer to the minimum, as supported by an energy calculation. Differing conformations of 1-deoxymannojirimycin were also observed: a (4)C(1) and (1)C(4) conformation in dGMII and hERMI, respectively. Thus, these two alpha-mannosidase classes distort these inhibitors in distinct manners. This is likely indicative of the binding characteristics of the two different catalytic mechanisms of these enzymes.

  • Organizational Affiliation

    Department of Medical Biophysics, University of Toronto, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-mannosidase II1,045Drosophila melanogasterMutation(s): 0 
Find proteins for Q24451 (Drosophila melanogaster)
Explore Q24451 
Go to UniProtKB:  Q24451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24451
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
KIF Binding MOAD:  1PS3 Ki: 5.20e+6 (nM) from 1 assay(s)
PDBBind:  1PS3 Ki: 5.20e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.089α = 90
b = 109.803β = 90
c = 138.896γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary