Crystal Structure of Human Glycogenin-1 (GYG1) Tyr195pIPhe mutant complexed with manganese and UDP

Experimental Data Snapshot

  • Resolution: 2.38 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

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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: https://doi.org/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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
263Homo sapiensMutation(s): 1 
Gene Names: GYG1GYG
UniProt & NIH Common Fund Data Resources
Find proteins for P46976 (Homo sapiens)
Explore P46976 
Go to UniProtKB:  P46976
GTEx:  ENSG00000163754 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46976
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PHI
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.38 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.17α = 90
b = 81.05β = 90
c = 111.2γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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