Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 79.43 kDa 
• Atom Count: 5456 
• Residue Count: 616 
• Unique protein chains: 1

1Z84

X-ray structure of galt-like protein from arabidopsis thaliana at5g18200

• DOI: 10.2210/pdb1Z84/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-03-29 Released: 2005-04-19 
• Deposition Author(s): Mccoy, J.G., Bitto, E., Phillips Jr., G.N., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.231 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Structure and Mechanism of an ADP-Glucose Phosphorylase from Arabidopsis thaliana

MCCOY, J.G., ARABSHAHI, A., BITTO, E., BINGMAN, C.A., RUZICKA, F.J., FREY, P.A., PHILLIPS JR., G.N.

(2006) Biochemistry 45: 3154-3162

• PubMed: 16519510 
• DOI: 10.1021/bi052232m
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The X-ray crystal structure of the At5g18200.1 protein has been determined to a nominal resolution of 2.30 A. The structure has a histidine triad (HIT)-like fold containing two distinct HIT-like motifs. The sequence of At5g18200.1 indicates a distant family relationship to the Escherichia coli galactose-1-P uridylyltransferase (GalT): the determined structure of the At5g18200.1 protein confirms this relationship. The At5g18200.1 protein does not demonstrate GalT activity but instead catalyzes adenylyl transfer in the reaction of ADP-glucose with various phosphates. The best acceptor among those evaluated is phosphate itself; thus, the At5g18200.1 enzyme appears to be an ADP-glucose phosphorylase. The enzyme catalyzes the exchange of (14)C between ADP-[(14)C]glucose and glucose-1-P in the absence of phosphate. The steady state kinetics of exchange follows the ping-pong bi-bi kinetic mechanism, with a k(cat) of 4.1 s(-)(1) and K(m) values of 1.4 and 83 microM for ADP-[(14)C]glucose and glucose-1-P, respectively, at pH 8.5 and 25 degrees C. The overall reaction of ADP-glucose with phosphate to produce ADP and glucose-1-P follows ping-pong bi-bi steady state kinetics, with a k(cat) of 2.7 s(-)(1) and K(m) values of 6.9 and 90 microM for ADP-glucose and phosphate, respectively, at pH 8.5 and 25 degrees C. The kinetics are consistent with a double-displacement mechanism that involves a covalent adenylyl-enzyme intermediate. The X-ray crystal structure of this intermediate was determined to 1.83 A resolution and shows the AMP group bonded to His(186). The value of K(eq) in the direction of ADP and glucose-1-P formation is 5.0 at pH 7.0 and 25 degrees C in the absence of a divalent metal ion, and it is 40 in the presence of 1 mM MgCl(2).

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
galactose-1-phosphate uridyl transferase-like protein	A, B	351	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At5g18200, MRG7.16 EC: 2.7.7
Find proteins for Q9FK51 (Arabidopsis thaliana) Go to UniProtKB:  Q9FK51

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	A, B	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	A, B	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.231 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.037	α = 90
b = 95.65	β = 90
c = 110.918	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-29 
• Released Date: 2005-04-19 
Deposition Author(s): Mccoy, J.G., Bitto, E., Phillips Jr., G.N., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Revision History 

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description