4KQ2

Glucose1,2cyclic phosphate bound activated state of Yeast Glycogen Synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.USA 110: 20976-20981

  • DOI: 10.1073/pnas.1310106111
  • Primary Citation of Related Structures:  4KQ1, 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 gluco ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gsy2p
A, B, C, D
724Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: GSY2
EC: 2.4.1.11
Find proteins for P27472 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P27472
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6P
Query on G6P

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-GLUCOSE-6-PHOSPHATE
C6 H13 O9 P
NBSCHQHZLSJFNQ-DVKNGEFBSA-N
 Ligand Interaction
U5P
Query on U5P

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Download CCD File 
A, B, C, D
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
1S3
Query on 1S3

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Download CCD File 
C
(2R,3aR,5R,6S,7S,7aR)-5-(hydroxymethyl)tetrahydro-3aH-[1,3,2]dioxaphospholo[4,5-b]pyran-2,6,7-triol 2-oxide
Glucose1,2cyclic phosphate
C6 H11 O8 P
PUJJEEQZLDDQPG-VFUOTHLCSA-N
 Ligand Interaction
BA
Query on BA

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Download CCD File 
A, B, C, D
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B, C, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 193.490α = 90.00
b = 203.978β = 90.00
c = 206.307γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
HKL-3000data reduction
REFMACrefinement
HKL-3000data collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Structure summary
  • Version 1.3: 2017-11-15
    Type: Refinement description