Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.19 kDa 
• Atom Count: 5178 
• Residue Count: 575 
• Unique protein chains: 1

3UIE

Crystal structure of adenosine 5'-phosphosulfate kinase from Arabidopsis Thaliana in Complex with AMPPNP and APS

• DOI: 10.2210/pdb3UIE/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-04 Released: 2012-01-25 
• Deposition Author(s): Ravilious, G.E., Jez, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.201 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Structural basis and evolution of redox regulation in plant adenosine-5'-phosphosulfate kinase.

Ravilious, G.E., Nguyen, A., Francois, J.A., Jez, J.M.

(2012) Proc Natl Acad Sci U S A 109: 309-314

• PubMed: 22184237 
• DOI: 10.1073/pnas.1115772108
• Primary Citation of Related Structures:  
  3UIE


• PubMed Abstract: 
  

Adenosine-5'-phosphosulfate (APS) kinase (APSK) catalyzes the phosphorylation of APS to 3'-phospho-APS (PAPS). In Arabidopsis thaliana, APSK is essential for reproductive viability and competes with APS reductase to partition sulfate between the primary and secondary branches of the sulfur assimilatory pathway; however, the biochemical regulation of APSK is poorly understood. The 1.8-Å resolution crystal structure of APSR from A. thaliana (AtAPSK) in complex with β,γ-imidoadenosine-5'-triphosphate, Mg(2+), and APS provides a view of the Michaelis complex for this enzyme and reveals the presence of an intersubunit disulfide bond between Cys86 and Cys119. Functional analysis of AtAPSK demonstrates that reduction of Cys86-Cys119 resulted in a 17-fold higher k(cat)/K(m) and a 15-fold increase in K(i) for substrate inhibition by APS compared with the oxidized enzyme. The C86A/C119A mutant was kinetically similar to the reduced WT enzyme. Gel- and activity-based titrations indicate that the midpoint potential of the disulfide in AtAPSK is comparable to that observed in APS reductase. Both cysteines are invariant among the APSK from plants, but not other organisms, which suggests redox-control as a unique regulatory feature of the plant APSK. Based on structural, functional, and sequence analyses, we propose that the redox-sensitive APSK evolved after bifurcation of the sulfur assimilatory pathway in the green plant lineage and that changes in redox environment resulting from oxidative stresses may affect partitioning of APS into the primary and secondary thiol metabolic routes by having opposing effects on APSK and APS reductase in plants.

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Organizational Affiliation: 

Department of Biology, Washington University, St. Louis, MO 63130, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylyl-sulfate kinase 1, chloroplastic	A, B, C	200	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AKN1, At2g14750, F26C24.11, T6B13.1, APK1 EC: 2.7.1.25
Find proteins for Q43295 (Arabidopsis thaliana) Explore Q43295  Go to UniProtKB:  Q43295

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	A, B, C	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ADX	A, B, C	ADENOSINE-5'-PHOSPHOSULFATE C10 H14 N5 O10 P S IRLPACMLTUPBCL-KQYNXXCUSA-N
MG	A, B, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.201 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.137	α = 90
b = 95.313	β = 114.08
c = 73.327	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-04 
• Released Date: 2012-01-25 
Deposition Author(s): Ravilious, G.E., Jez, J.M.

Revision History 

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description