Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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)

Macromolecule Content

• Total Structure Weight: 60.91 kDa 
• Atom Count: 4740 
• Modelled Residue Count: 515 
• Deposited Residue Count: 526 
• Unique protein chains: 1

3U2W

Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and glucose or a glucal species

• PDB DOI: 10.2210/pdb3U2W/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-10-04 Released: 2011-11-02 
• Deposition Author(s): Chaikuad, A., Froese, D.S., Krysztofinska, E., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Oppermann, U., Yue, W.W., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.190 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Literature

Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis.

Chaikuad, A., Froese, D.S., Berridge, G., von Delft, F., Oppermann, U., Yue, W.W.

(2011) Proc Natl Acad Sci U S A 108: 21028-21033

• PubMed: 22160680 
• DOI: 10.1073/pnas.1113921108
• Primary Citation of Related Structures:  
  3Q4S, 3QVB, 3RMV, 3RMW, 3T7M, 3T7N, 3T7O, 3U2T, 3U2U, 3U2V, 3U2W


• PubMed Abstract: 
  

Glycogenin initiates the synthesis of a maltosaccharide chain covalently attached to itself on Tyr195 via a stepwise glucosylation reaction, priming glycogen synthesis. We have captured crystallographic snapshots of human glycogenin during its reaction cycle, revealing a dynamic conformational switch between ground and active states mediated by the sugar donor UDP-glucose. This switch includes the ordering of a polypeptide stretch containing Tyr195, and major movement of an approximately 30-residue "lid" segment covering the active site. The rearranged lid guides the nascent maltosaccharide chain into the active site in either an intra- or intersubunit mode dependent upon chain length and steric factors and positions the donor and acceptor sugar groups for catalysis. The Thr83Met mutation, which causes glycogen storage disease XV, is conformationally locked in the ground state and catalytically inactive. Our data highlight the conformational plasticity of glycogenin and coexistence of two modes of glucosylation as integral to its catalytic mechanism.

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Organizational Affiliation: 

Structural Genomics Consortium, Old Road Research Campus Building, Oxford, United Kingdom OX3 7DQ.

Macromolecules

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	D [auth A], J [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
GLC	G [auth A], L [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
LCN	H [auth A]	1,5-anhydro-D-arabino-hex-1-enitol C6 H10 O5 CXKKSSKKIOZUNR-HSUXUTPPSA-N
GOL	E [auth A], F [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.190 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.29	α = 90
b = 80.18	β = 100.67
c = 69.53	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-04 
• Released Date: 2011-11-02 
Deposition Author(s): Chaikuad, A., Froese, D.S., Krysztofinska, E., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Oppermann, U., Yue, W.W., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2011-12-28
  Changes: Database references
• Version 1.2: 2012-01-11
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary