5CB8

Crystal structure of Adenosine-5'-phosphosulfate kinase in complex with APS and sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recapitulating the Structural Evolution of Redox Regulation in Adenosine 5'-Phosphosulfate Kinase from Cyanobacteria to Plants.

Herrmann, J.Nathin, D.Lee, S.G.Sun, T.Jez, J.M.

(2015) J.Biol.Chem. 290: 24705-24714

  • DOI: 10.1074/jbc.M115.679514
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In plants, adenosine 5'-phosphosulfate (APS) kinase (APSK) is required for reproductive viability and the production of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfur donor in specialized metabolism. Previous studies of the APSK from Arabid ...

    In plants, adenosine 5'-phosphosulfate (APS) kinase (APSK) is required for reproductive viability and the production of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfur donor in specialized metabolism. Previous studies of the APSK from Arabidopsis thaliana (AtAPSK) identified a regulatory disulfide bond formed between the N-terminal domain (NTD) and a cysteine on the core scaffold. This thiol switch is unique to mosses, gymnosperms, and angiosperms. To understand the structural evolution of redox control of APSK, we investigated the redox-insensitive APSK from the cyanobacterium Synechocystis sp. PCC 6803 (SynAPSK). Crystallographic analysis of SynAPSK in complex with either APS and a non-hydrolyzable ATP analog or APS and sulfate revealed the overall structure of the enzyme, which lacks the NTD found in homologs from mosses and plants. A series of engineered SynAPSK variants reconstructed the structural evolution of the plant APSK. Biochemical analyses of SynAPSK, SynAPSK H23C mutant, SynAPSK fused to the AtAPSK NTD, and the fusion protein with the H23C mutation showed that the addition of the NTD and cysteines recapitulated thiol-based regulation. These results reveal the molecular basis for structural changes leading to the evolution of redox control of APSK in the green lineage from cyanobacteria to plants.


    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
Probable adenylyl-sulfate kinase
A, B
197Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: cysC
EC: 2.7.1.25
Find proteins for P72940 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P72940
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADX
Query on ADX

Download SDF File 
Download CCD File 
A, B
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
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADXKi: 18200 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.155 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 140.756α = 90.00
b = 140.756β = 90.00
c = 140.756γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-10-28
    Type: Database references