Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 202163.59 
• Atom Count: 13550 
• Residue Count: 1804 
• Unique protein chains: 1

1YP4

Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with ADP-glucose

• DOI: 10.2210/pdb1YP4/pdb

• Classification: TRANSFERASE
• Organism(s): Solanum tuberosum
• Expression System: Escherichia coli


• Deposited: 2005-01-29 Released: 2005-03-15 
• Deposition Author(s): Jin, X., Ballicora, M.A., Preiss, J., Geiger, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.244 
• R-Value Work: 0.183 

Literature

Crystal structure of potato tuber ADP-glucose pyrophosphorylase.

Jin, X., Ballicora, M.A., Preiss, J., Geiger, J.H.

(2005) Embo J. 24: 694-704

• PubMed: 15692569 
• DOI: 10.1038/sj.emboj.7600551
• Primary Citation of Related Structures:  
  1YP3, 1YP2


• PubMed Abstract: 
  

ADP-glucose pyrophosphorylase catalyzes the first committed and rate-limiting step in starch biosynthesis in plants and glycogen biosynthesis in bacteria. It is the enzymatic site for regulation of storage polysaccharide accumulation in plants and bacteria, being allosterically activated or inhibited by metabolites of energy flux. We report the first atomic resolution structure of ADP-glucose pyrophosphorylase. Crystals of potato tuber ADP-glucose pyrophosphorylase alpha subunit were grown in high concentrations of sulfate, resulting in the sulfate-bound, allosterically inhibited form of the enzyme. The N-terminal catalytic domain resembles a dinucleotide-binding Rossmann fold and the C-terminal domain adopts a left-handed parallel beta helix that is involved in cooperative allosteric regulation and a unique oligomerization. We also report structures of the enzyme in complex with ATP and ADP-glucose. Communication between the regulator-binding sites and the active site is both subtle and complex and involves several distinct regions of the enzyme including the N-terminus, the glucose-1-phosphate-binding site, and the ATP-binding site. These structures provide insights into the mechanism for catalysis and allosteric regulation of the enzyme.

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Organizational Affiliation: 

Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucose-1-phosphate adenylyltransferase small subunit	A, B, C, D	451	Solanum tuberosum	Mutation(s): 0  EC: 2.7.7.27
Find proteins for P23509 (Solanum tuberosum) Go to UniProtKB:  P23509

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ADP	A, C	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ADQ	B	ADENOSINE-5'-DIPHOSPHATE-GLUCOSE ADENOSINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER C16 H25 N5 O15 P2 WFPZSXYXPSUOPY-ROYWQJLOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.244 
• R-Value Work: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 79.857	α = 90.00
b = 137.964	β = 112.91
c = 90.832	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-29 
• Released Date: 2005-03-15 
• Deposition Author(s): Jin, X., Ballicora, M.A., Preiss, J., Geiger, J.H.

Revision History 

• Version 1.0: 2005-03-15
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance