1RZU

Crystal structure of the glycogen synthase from A. tumefaciens in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation.

Buschiazzo, A.Ugalde, J.E.Guerin, M.E.Shepard, W.Ugalde, R.A.Alzari, P.M.

(2004) Embo J. 23: 3196-3205

  • DOI: 10.1038/sj.emboj.7600324
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycogen and starch are the major readily accessible energy storage compounds in nearly all living organisms. Glycogen is a very large branched glucose homopolymer containing about 90% alpha-1,4-glucosidic linkages and 10% alpha-1,6 linkages. Its syn ...

    Glycogen and starch are the major readily accessible energy storage compounds in nearly all living organisms. Glycogen is a very large branched glucose homopolymer containing about 90% alpha-1,4-glucosidic linkages and 10% alpha-1,6 linkages. Its synthesis and degradation constitute central pathways in the metabolism of living cells regulating a global carbon/energy buffer compartment. Glycogen biosynthesis involves the action of several enzymes among which glycogen synthase catalyzes the synthesis of the alpha-1,4-glucose backbone. We now report the first crystal structure of glycogen synthase in the presence and absence of adenosine diphosphate. The overall fold and the active site architecture of the protein are remarkably similar to those of glycogen phosphorylase, indicating a common catalytic mechanism and comparable substrate-binding properties. In contrast to glycogen phosphorylase, glycogen synthase has a much wider catalytic cleft, which is predicted to undergo an important interdomain 'closure' movement during the catalytic cycle. The structures also provide useful hints to shed light on the allosteric regulation mechanisms of yeast/mammalian glycogen synthases.


    Related Citations: 
    • Preliminary crystallographic studies of glycogen synthase from Agrobacterium tumefaciens
      Guerin, M.E.,Buschiazzo, A.,Ugalde, J.E.,Ugalde, R.A.,Alzari, P.M.
      (2003) Acta Crystallogr.,Sect.D 59: 526


    Organizational Affiliation

    Unité de Biochimie Structurale, URA 2185 CNRS, Institut Pasteur, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen synthase 1
A, B
485Rhizobium radiobacterMutation(s): 0 
Gene Names: glgA1 (glgA)
EC: 2.4.1.21
Find proteins for P0A3F3 (Rhizobium radiobacter)
Go to UniProtKB:  P0A3F3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.357α = 90.00
b = 88.115β = 98.19
c = 84.463γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
TRUNCATEdata scaling
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description