6BQ6

Crystal structure of Medicago truncatula Thermospermine Synthase (MtTSPS) in complex with thermospermine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of thermospermine synthase fromMedicago truncatulaand substrate discriminatory features of plant aminopropyltransferases.

Sekula, B.Dauter, Z.

(2018) Biochem. J. 475: 787-802

  • DOI: 10.1042/BCJ20170900
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polyamines are linear polycationic compounds that play a crucial role in the growth and development of higher plants. One triamine (spermidine, SPD) and two tetraamine isomers (spermine, SPM, and thermospermine, TSPM) are obtained by the transfer of ...

    Polyamines are linear polycationic compounds that play a crucial role in the growth and development of higher plants. One triamine (spermidine, SPD) and two tetraamine isomers (spermine, SPM, and thermospermine, TSPM) are obtained by the transfer of the aminopropyl group from decarboxylated S -adenosylmethionine to putrescine and SPD. These reactions are catalyzed by the specialized aminopropyltransferases. In that respect, plants are unique eukaryotes that have independently evolved two enzymes, thermospermine synthase (TSPS), encoded by the gene ACAULIS5 , and spermine synthase, which produce TSPM and SPM, respectively. In this work, we structurally characterize the ACAULIS5 gene product, TSPS, from the model legume plant Medicago truncatula ( Mt ). Six crystal structures of Mt TSPS - one without ligands and five in complexes with either reaction substrate (SPD), reaction product (TSPM), or one of three cofactor analogs (5'-methylthioadenosine, S -adenosylthiopropylamine, and adenosine) - give detailed insights into the biosynthesis of TSPM. Combined with small-angle X-ray scattering data, the crystal structures show that Mt TSPS is a symmetric homotetramer with an interdomain eight-stranded β-barrel. Such an assembly and the presence of a hinge-like feature between N-terminal and C-terminal domains give the protein additional flexibility which potentially improves loading substrates and discarding products after the catalytic event. We also discuss the sequence and structural features around the active site of the plant aminopropyltransferases that distinguish them from each other and determine their characteristic substrate discrimination.


    Organizational Affiliation

    Synchrotron Radiation Research Section of Macromolecular Crystallography Laboratory, National Cancer Institute, South Cass Avenue 9700, Argonne, IL 60439, U.S.A. bartosz.sekula@nih.gov.,Synchrotron Radiation Research Section of Macromolecular Crystallography Laboratory, National Cancer Institute, South Cass Avenue 9700, Argonne, IL 60439, U.S.A.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermospermine synthase
A, B
331Medicago truncatulaMutation(s): 0 
Gene Names: 11439099
EC: 2.5.1.16
Find proteins for G7K2D1 (Medicago truncatula)
Go to UniProtKB:  G7K2D1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
TER
Query on TER

Download SDF File 
Download CCD File 
A, B
N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE
THERMOSPERMINE; PA(334)
C10 H26 N4
DODDBCGMRAFLEB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.172 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.293α = 90.00
b = 80.293β = 90.00
c = 163.245γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-27 
  • Released Date: 2018-02-28 
  • Deposition Author(s): Sekula, B., Dauter, Z.

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesThe Intramural Research Program

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Database references
  • Version 1.2: 2018-05-02
    Type: Data collection, Database references