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 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 3.1 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: https://doi.org/10.1038/s41598-017-04539-2
  • Primary Citation of Related Structures:  
    5MEK, 5MEX

  • 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.) 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosolic sulfotransferase 18322Arabidopsis thalianaMutation(s): 0 
Gene Names: SOT18ST5BAt1g74090F2P9.4
EC: 2.8.2 (PDB Primary Data), 2.8.2.38 (UniProt)
UniProt
Find proteins for Q9C9C9 (Arabidopsis thaliana)
Explore Q9C9C9 
Go to UniProtKB:  Q9C9C9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C9C9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAP
Query on PAP

Download Ideal Coordinates CCD File 
B [auth A]3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
GBBWIZKLHXYJOA-KQYNXXCUSA-N
SZZ
Query on SZZ

Download Ideal Coordinates CCD File 
C [auth A]Sinigrin
C10 H17 N O9 S2
PHZOWSSBXJXFOR-PTGZALFTSA-N
BU2
Query on BU2

Download Ideal Coordinates CCD File 
N [auth A]1,3-BUTANEDIOL
C4 H10 O2
PUPZLCDOIYMWBV-BYPYZUCNSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.82α = 90
b = 63.82β = 90
c = 209.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 2.0: 2017-09-06
    Changes: Advisory, Atomic model, Author supporting evidence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations
  • Version 3.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description