4RKK

Structure of a product bound phosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural mechanism of laforin function in glycogen dephosphorylation and lafora disease.

Raththagala, M.Brewer, M.K.Parker, M.W.Sherwood, A.R.Wong, B.K.Hsu, S.Bridges, T.M.Paasch, B.C.Hellman, L.M.Husodo, S.Meekins, D.A.Taylor, A.O.Turner, B.D.Auger, K.D.Dukhande, V.V.Chakravarthy, S.Sanz, P.Woods, V.L.Li, S.Vander Kooi, C.W.Gentry, M.S.

(2015) Mol Cell 57: 261-272

  • DOI: https://doi.org/10.1016/j.molcel.2014.11.020
  • Primary Citation of Related Structures:  
    4RKK

  • PubMed Abstract: 

    Glycogen is the major mammalian glucose storage cache and is critical for energy homeostasis. Glycogen synthesis in neurons must be tightly controlled due to neuronal sensitivity to perturbations in glycogen metabolism. Lafora disease (LD) is a fatal, congenital, neurodegenerative epilepsy. Mutations in the gene encoding the glycogen phosphatase laforin result in hyperphosphorylated glycogen that forms water-insoluble inclusions called Lafora bodies (LBs). LBs induce neuronal apoptosis and are the causative agent of LD. The mechanism of glycogen dephosphorylation by laforin and dysfunction in LD is unknown. We report the crystal structure of laforin bound to phosphoglucan product, revealing its unique integrated tertiary and quaternary structure. Structure-guided mutagenesis combined with biophysical and biochemical analyses reveal the basis for normal function of laforin in glycogen metabolism. Analyses of LD patient mutations define the mechanism by which subsets of mutations disrupt laforin function. These data provide fundamental insights connecting glycogen metabolism to neurodegenerative disease.


  • Organizational Affiliation

    Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LaforinA,
B [auth C]
332Homo sapiensMutation(s): 1 
Gene Names: EPM2A
EC: 3.1.3 (PDB Primary Data), 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95278 (Homo sapiens)
Explore O95278 
Go to UniProtKB:  O95278
PHAROS:  O95278
GTEx:  ENSG00000112425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95278
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC [auth B],
E,
F
6N/A
Glycosylation Resources
GlyTouCan:  G91368RN
GlyCosmos:  G91368RN
GlyGen:  G91368RN
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
D, G
3N/A
Glycosylation Resources
GlyTouCan:  G96370VA
GlyCosmos:  G96370VA
GlyGen:  G96370VA
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
H
4N/A
Glycosylation Resources
GlyTouCan:  G87171PZ
GlyCosmos:  G87171PZ
GlyGen:  G87171PZ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.706α = 90
b = 78.706β = 90
c = 321.124γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-07
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references, Structure summary