5MEX

Sulphotransferase-18 from Arabidopsis thaliana in complex with 3'-phosphoadenosine 5'-phosphate (PAP)and sinigrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural and biochemical studies of sulphotransferase 18 from Arabidopsis thaliana explain its substrate specificity and reaction mechanism.

Hirschmann, F.Krause, F.Baruch, P.Chizhov, I.Mueller, J.W.Manstein, D.J.Papenbrock, J.Fedorov, R.

(2017) Sci Rep 7: 4160-4160

  • DOI: 10.1038/s41598-017-04539-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sulphotransferases are a diverse group of enzymes catalysing the transfer of a sulfuryl group from 3'-phosphoadenosine 5'-phosphosulphate (PAPS) to a broad range of secondary metabolites. They exist in all kingdoms of life. In Arabidopsis thaliana (L ...

    Sulphotransferases are a diverse group of enzymes catalysing the transfer of a sulfuryl group from 3'-phosphoadenosine 5'-phosphosulphate (PAPS) to a broad range of secondary metabolites. They exist in all kingdoms of life. In Arabidopsis thaliana (L.) Heynh. twenty-two sulphotransferase (SOT) isoforms were identified. Three of those are involved in glucosinolate (Gl) biosynthesis, glycosylated sulphur-containing aldoximes containing chemically different side chains, whose break-down products are involved in stress response against herbivores, pathogens, and abiotic stress. To explain the differences in substrate specificity of desulpho (ds)-Gl SOTs and to understand the reaction mechanism of plant SOTs, we determined the first high-resolution crystal structure of the plant ds-Gl SOT AtSOT18 in complex with 3'-phosphoadenosine 5'-phosphate (PAP) alone and together with the Gl sinigrin. These new structural insights into the determination of substrate specificity were complemented by mutagenesis studies. The structure of AtSOT18 invigorates the similarity between plant and mammalian sulphotransferases, which illustrates the evolutionary conservation of this multifunctional enzyme family. We identified the essential residues for substrate binding and catalysis and demonstrated that the catalytic mechanism is conserved between human and plant enzymes. Our study indicates that the loop-gating mechanism is likely to be a source of the substrate specificity in plants.


    Organizational Affiliation

    Institute of Botany, Leibniz University Hannover, Herrenhäuserstr. 2, D-30419, Hannover, Germany. Jutta.Papenbrock@botanik.uni-hannover.de.,Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625, Hannover, Germany.,Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625, Hannover, Germany.,Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Botany, Leibniz University Hannover, Herrenhäuserstr. 2, D-30419, Hannover, Germany.,Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham, B15 2TH, UK.,Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625, Hannover, Germany. Fedorov.Roman@mh-hannover.de.,Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625, Hannover, Germany. Fedorov.Roman@mh-hannover.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytosolic sulfotransferase 18
A
322Arabidopsis thalianaMutation(s): 0 
Gene Names: SOT18 (ST5B)
EC: 2.8.2.38
Find proteins for Q9C9C9 (Arabidopsis thaliana)
Go to UniProtKB:  Q9C9C9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SZZ
Query on SZZ

Download SDF File 
Download CCD File 
A
Sinigrin
C10 H17 N O9 S2
PHZOWSSBXJXFOR-PTGZALFTSA-N
 Ligand Interaction
BU2
Query on BU2

Download SDF File 
Download CCD File 
A
1,3-BUTANEDIOL
C4 H10 O2
PUPZLCDOIYMWBV-BYPYZUCNSA-N
 Ligand Interaction
PAP
Query on PAP

Download SDF File 
Download CCD File 
A
3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
GBBWIZKLHXYJOA-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.820α = 90.00
b = 63.820β = 90.00
c = 209.970γ = 90.00
Software Package:
Software NamePurpose
SADABSdata scaling
AMoREphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyPA 764/10-1
German Research FoundationGermanyFE 1510/2-1

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 2.0: 2017-09-06
    Type: Advisory, Atomic model, Author supporting evidence