6EQJ

Crystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant, apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Palladium-mediated enzyme activation suggests multiphase initiation of glycogenesis.

Bilyard, M.K.Bailey, H.J.Raich, L.Gafitescu, M.A.Machida, T.Iglesias-Fernandez, J.Lee, S.S.Spicer, C.D.Rovira, C.Yue, W.W.Davis, B.G.

(2018) Nature 563: 235-240

  • DOI: 10.1038/s41586-018-0644-7
  • Primary Citation of Related Structures:  
    6EQJ, 6EQL

  • PubMed Abstract: 
  • Biosynthesis of glycogen, the essential glucose (and hence energy) storage molecule in humans, animals and fungi 1 , is initiated by the glycosyltransferase enzyme, glycogenin (GYG). Deficiencies in glycogen formation cause neurodegenerative a ...

    Biosynthesis of glycogen, the essential glucose (and hence energy) storage molecule in humans, animals and fungi 1 , is initiated by the glycosyltransferase enzyme, glycogenin (GYG). Deficiencies in glycogen formation cause neurodegenerative and metabolic disease 2-4 , and mouse knockout 5 and inherited human mutations 6 of GYG impair glycogen synthesis. GYG acts as a 'seed core' for the formation of the glycogen particle by catalysing its own stepwise autoglucosylation to form a covalently bound gluco-oligosaccharide chain at initiation site Tyr 195. Precise mechanistic studies have so far been prevented by an inability to access homogeneous glycoforms of this protein, which unusually acts as both catalyst and substrate. Here we show that unprecedented direct access to different, homogeneously glucosylated states of GYG can be accomplished through a palladium-mediated enzyme activation 'shunt' process using on-protein C-C bond formation. Careful mimicry of GYG intermediates recapitulates catalytic activity at distinct stages, which in turn allows discovery of triphasic kinetics and substrate plasticity in GYG's use of sugar substrates. This reveals a tolerant but 'proof-read' mechanism that underlies the precision of this metabolic process. The present demonstration of direct, chemically controlled access to intermediate states of active enzymes suggests that such ligation-dependent activation could be a powerful tool in the study of mechanism.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, Oxford, UK. ben.davis@chem.ox.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogenin-1 A263Homo sapiensMutation(s): 0 
Gene Names: GYG1GYG
EC: 2.4.1.186
Find proteins for P46976 (Homo sapiens)
Explore P46976 
Go to UniProtKB:  P46976
NIH Common Fund Data Resources
PHAROS:  P46976
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHI
Query on PHI
AL-PEPTIDE LINKINGC9 H10 I N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.03α = 90
b = 101.02β = 90
c = 49.42γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.3: 2018-11-14
    Changes: Data collection, Database references