Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 30.03 kDa 
• Atom Count: 1956 
• Residue Count: 245 
• Unique protein chains: 1

6EQJ

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

• DOI: 10.2210/pdb6EQJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-13 Released: 2017-12-20 
• Deposition Author(s): Bailey, H.J., Kopec, J., Bilyard, M.K., Bezerra, G.A., Seo Lee, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Davis, B.G., Yue, W.W.

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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 

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

• PubMed: 30356213 
• 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 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.

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Organizational Affiliation: 

Department of Chemistry, University of Oxford, Oxford, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogenin-1	A	263	Homo sapiens	Mutation(s): 0  Gene Names: GYG1, GYG EC: 2.4.1.186
Find proteins for P46976 (Homo sapiens) Explore P46976  Go to UniProtKB:  P46976
NIH Common Fund Data Resources
PHAROS:  P46976 GTEx:  ENSG00000163754

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHI	A	L-PEPTIDE LINKING	C9 H10 I N O2		PHE

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 = 59.03	α = 90
b = 101.02	β = 90
c = 49.42	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-10-13 
• Released Date: 2017-12-20 
Deposition Author(s): Bailey, H.J., Kopec, J., Bilyard, M.K., Bezerra, G.A., Seo Lee, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Davis, B.G., Yue, W.W.

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