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: 1.79 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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This is version 1.2 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 U S A 109: 309-314

  • DOI: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylyl-sulfate kinase 1, chloroplastic
A, B, C
200Arabidopsis thalianaMutation(s): 0 
Gene Names: AKN1At2g14750F26C24.11T6B13.1
EC: 2.7.1.25
UniProt
Find proteins for Q43295 (Arabidopsis thaliana)
Explore Q43295 
Go to UniProtKB:  Q43295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ43295
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ADX
Query on ADX

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
ADENOSINE-5'-PHOSPHOSULFATE
C10 H14 N5 O10 P S
IRLPACMLTUPBCL-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth 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 = 121.137α = 90
b = 95.313β = 114.08
c = 73.327γ = 90
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary