Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 104.72 kDa 
• Atom Count: 8076 
• Modelled Residue Count: 919 
• Deposited Residue Count: 938 
• Unique protein chains: 1

2ICY

Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UDP-glucose

• PDB DOI: 10.2210/pdb2ICY/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-13 Released: 2006-10-03 
• Deposition Author(s): McCoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.223 
• R-Value Work: 0.183 

Literature

Structure and Dynamics of UDP-Glucose Pyrophosphorylase from Arabidopsis thaliana with Bound UDP-Glucose and UTP.

McCoy, J.G., Bitto, E., Bingman, C.A., Wesenberg, G.E., Bannen, R.M., Kondrashov, D.A., Phillips Jr., G.N.

(2007) J Mol Biol 366: 830-841

• PubMed: 17178129 
• DOI: 10.1016/j.jmb.2006.11.059
• Primary Citation of Related Structures:  
  1Z90, 2ICX, 2ICY


• PubMed Abstract: 
  

The structure of the UDP-glucose pyrophosphorylase encoded by Arabidopsis thaliana gene At3g03250 has been solved to a nominal resolution of 1.86 Angstroms. In addition, the structure has been solved in the presence of the substrates/products UTP and UDP-glucose to nominal resolutions of 1.64 Angstroms and 1.85 Angstroms. The three structures revealed a catalytic domain similar to that of other nucleotidyl-glucose pyrophosphorylases with a carboxy-terminal beta-helix domain in a unique orientation. Conformational changes are observed between the native and substrate-bound complexes. The nucleotide-binding loop and the carboxy-terminal domain, including the suspected catalytically important Lys360, move in and out of the active site in a concerted fashion. TLS refinement was employed initially to model conformational heterogeneity in the UDP-glucose complex followed by the use of multiconformer refinement for the entire molecule. Normal mode analysis generated atomic displacement predictions in good agreement in magnitude and direction with the observed conformational changes and anisotropic displacement parameters generated by TLS refinement. The structures and the observed dynamic changes provide insight into the ordered mechanism of this enzyme and previously described oligomerization effects on catalytic activity.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable UTP-glucose-1-phosphate uridylyltransferase 2	A, B	469	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At3g03250, T17B22.6, UGP2 EC: 2.7.7.9
UniProt
Find proteins for Q9M9P3 (Arabidopsis thaliana) Explore Q9M9P3  Go to UniProtKB:  Q9M9P3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG	D [auth A], E [auth B]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
U5P		URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.223 
• R-Value Work: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.008	α = 90
b = 59.712	β = 100.32
c = 89.762	γ = 90

Software Package:

Software Name	Purpose
HKL	data processing
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-09-13 
• Released Date: 2006-10-03 
Deposition Author(s): McCoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2006-10-03
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2015-09-09
  Changes: Version format compliance