4FXP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.954 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nucleotide binding site communication in Arabidopsis thaliana adenosine 5'-phosphosulfate kinase.

Ravilious, G.E.Jez, J.M.

(2012) J.Biol.Chem. 287: 30385-30394

  • DOI: 10.1074/jbc.M112.387001

  • PubMed Abstract: 
  • Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the ATP-dependent synthesis of adenosine 3'-phosphate 5'-phosphosulfate (PAPS), which is an essential metabolite for sulfur assimilation in prokaryotes and eukaryotes. Using APSK from Arabidopsis th ...

    Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the ATP-dependent synthesis of adenosine 3'-phosphate 5'-phosphosulfate (PAPS), which is an essential metabolite for sulfur assimilation in prokaryotes and eukaryotes. Using APSK from Arabidopsis thaliana, we examine the energetics of nucleotide binary and ternary complex formation and probe active site features that coordinate the order of ligand addition. Calorimetric analysis shows that binding can occur first at either nucleotide site, but that initial interaction at the ATP/ADP site was favored and enhanced affinity for APS in the second site by 50-fold. The thermodynamics of the two possible binding models (i.e. ATP first versus APS first) differs and implies that active site structural changes guide the order of nucleotide addition. The ligand binding analysis also supports an earlier suggestion of intermolecular interactions in the dimeric APSK structure. Crystallographic, site-directed mutagenesis, and energetic analyses of oxyanion recognition by the P-loop in the ATP/ADP binding site and the role of Asp(136), which bridges the ATP/ADP and APS/PAPS binding sites, suggest how the ordered nucleotide binding sequence and structural changes are dynamically coordinated for catalysis.


    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 2 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADXKd: 80400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.954 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 120.948α = 90.00
b = 92.348β = 113.52
c = 73.183γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
PHASERphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2013-01-09
    Type: Database references