3UIE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.794 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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.USA 109: 309-314

  • DOI: 10.1073/pnas.1115772108

  • 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 prim ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylyl-sulfate kinase 1, chloroplastic
A, B, C
200Arabidopsis thalianaMutation(s): 0 
Gene Names: APK1 (AKN1)
EC: 2.7.1.25
Find proteins for Q43295 (Arabidopsis thaliana)
Go to UniProtKB:  Q43295
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADX
Query on ADX

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-PHOSPHOSULFATE
C10 H14 N5 O10 P S
IRLPACMLTUPBCL-KQYNXXCUSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.794 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 121.137α = 90.00
b = 95.313β = 114.08
c = 73.327γ = 90.00
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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