3EO3

Crystal structure of the N-acetylmannosamine kinase domain of human GNE protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the N-acetylmannosamine kinase domain of GNE.

Tong, Y.Tempel, W.Nedyalkova, L.Mackenzie, F.Park, H.W.

(2009) PLoS One 4: e7165-e7165

  • DOI: https://doi.org/10.1371/journal.pone.0007165
  • Primary Citation of Related Structures:  
    3EO3

  • PubMed Abstract: 

    UDP-GlcNAc 2-epimerase/ManNAc 6-kinase, GNE, is a bi-functional enzyme that plays a key role in sialic acid biosynthesis. Mutations of the GNE protein cause sialurea or autosomal recessive inclusion body myopathy/Nonaka myopathy. GNE is the only human protein that contains a kinase domain belonging to the ROK (repressor, ORF, kinase) family.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
A, B, C
333Homo sapiensMutation(s): 0 
Gene Names: GNEGLCNE
EC: 5.1.3.14 (PDB Primary Data), 2.7.1.60 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y223 (Homo sapiens)
Explore Q9Y223 
Go to UniProtKB:  Q9Y223
GTEx:  ENSG00000159921 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y223
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.946α = 90
b = 127.946β = 90
c = 127.247γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations