Crystal structure of yeast glycogen synthase in complex with uridine-5'-monophosphate

Experimental Data Snapshot

  • Resolution: 2.66 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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Structural basis for 2'-phosphate incorporation into glycogen by glycogen synthase.

Chikwana, V.M.Khanna, M.Baskaran, S.Tagliabracci, V.S.Contreras, C.J.Depaoli-Roach, A.Roach, P.J.Hurley, T.D.

(2013) Proc Natl Acad Sci U S A 110: 20976-20981

  • DOI: https://doi.org/10.1073/pnas.1310106111
  • Primary Citation of Related Structures:  
    4KQ1, 4KQ2, 4KQM

  • PubMed Abstract: 

    Glycogen is a glucose polymer that contains minor amounts of covalently attached phosphate. Hyperphosphorylation is deleterious to glycogen structure and can lead to Lafora disease. Recently, it was demonstrated that glycogen synthase catalyzes glucose-phosphate transfer in addition to its characteristic glucose transfer reaction. Glucose-1,2-cyclic-phosphate (GCP) was proposed to be formed from UDP-Glc breakdown and subsequently transferred, thus providing a source of phosphate found in glycogen. To gain further insight into the molecular basis for glucose-phosphate transfer, two structures of yeast glycogen synthase were determined; a 3.0-Å resolution structure of the complex with UMP/GCP and a 2.8-Å resolution structure of the complex with UDP/glucose. Structural superposition of the complexes revealed that the bound ligands and most active site residues are positioned similarly, consistent with the use of a common transfer mechanism for both reactions. The N-terminal domain of the UDP-glucose complex was found to be 13.3° more closed compared with a UDP complex. However, the UMP · GCP complex was 4.8° less closed than the glucose complex, which may explain the low efficiency of GCP transfer. Modeling of either α- or β-glucose or a mixture of both anomers can account for the observed electron density of the UDP-glucose complex. NMR studies of UDP-Glc hydrolysis by yeast glycogen synthase were used to verify the stereochemistry of the product, and they also showed synchronous GCP accumulation. The similarities in the active sites of glycogen synthase and glycogen phosphorylase support the idea of a common catalytic mechanism in GT-B enzymes independent of the specific reaction catalyzed.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
724Saccharomyces cerevisiae FostersOMutation(s): 2 
Gene Names: FOSTERSO_3265GSY2 YLR258W L8479.8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on U5P

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
C9 H13 N2 O9 P
Query on G6P

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
C6 H13 O9 P
Query on PEG

Download Ideal Coordinates CCD File 
G [auth B],
J [auth B],
M [auth C],
P [auth D]
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.66 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.089α = 90
b = 204.372β = 90
c = 206.446γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary