4MAF

Soybean ATP Sulfurylase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structure and mechanism of soybean ATP sulfurylase and the committed step in plant sulfur assimilation.

Herrmann, J., Ravilious, G.E., McKinney, S.E., Westfall, C.S., Lee, S.G., Baraniecka, P., Giovannetti, M., Kopriva, S., Krishnan, H.B., Jez, J.M.

(2014) J.Biol.Chem. 289: 10919-10929

  • DOI: 10.1074/jbc.M113.540401

  • PubMed Abstract: 

    • Enzymes of the sulfur assimilation pathway are potential targets for improving nutrient content and environmental stress responses in plants. The committed step in this pathway is catalyzed by ATP sulfurylase, which synthesizes adenosine 5'-phosphosu ...

    Enzymes of the sulfur assimilation pathway are potential targets for improving nutrient content and environmental stress responses in plants. The committed step in this pathway is catalyzed by ATP sulfurylase, which synthesizes adenosine 5'-phosphosulfate (APS) from sulfate and ATP. To better understand the molecular basis of this energetically unfavorable reaction, the x-ray crystal structure of ATP sulfurylase isoform 1 from soybean (Glycine max ATP sulfurylase) in complex with APS was determined. This structure revealed several highly conserved substrate-binding motifs in the active site and a distinct dimerization interface compared with other ATP sulfurylases but was similar to mammalian 3'-phosphoadenosine 5'-phosphosulfate synthetase. Steady-state kinetic analysis of 20 G. max ATP sulfurylase point mutants suggests a reaction mechanism in which nucleophilic attack by sulfate on the α-phosphate of ATP involves transition state stabilization by Arg-248, Asn-249, His-255, and Arg-349. The structure and kinetic analysis suggest that ATP sulfurylase overcomes the energetic barrier of APS synthesis by distorting nucleotide structure and identifies critical residues for catalysis. Mutations that alter sulfate assimilation in Arabidopsis were mapped to the structure, which provides a molecular basis for understanding their effects on the sulfur assimilation pathway.

    Organizational Affiliation: 

    From the Department of Biology, Washington University, St. Louis, Missouri 63130.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP sulfurylase
A, B, C, D, E, F, G, H
404Glycine maxMutation(s): 0 
Find proteins for Q8SAG1 (Glycine max)
Go to UniProtKB:  Q8SAG1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADX
Query on ADX
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ADENOSINE-5'-PHOSPHOSULFATE
C10 H14 N5 O10 P S
IRLPACMLTUPBCL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 204.268α = 90.00
b = 230.751β = 90.00
c = 159.197γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
HKL-3000data reduction
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references
  • Version 1.2: 2014-04-30
    Type: Database references