1JQ3

Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor.

Korolev, S.Ikeguchi, Y.Skarina, T.Beasley, S.Arrowsmith, C.Edwards, A.Joachimiak, A.Pegg, A.E.Savchenko, A.

(2002) Nat.Struct.Mol.Biol. 9: 27-31

  • DOI: 10.1038/nsb737
  • Primary Citation of Related Structures:  1INL

  • PubMed Abstract: 
  • Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has ...

    Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has been solved to 1.5 A resolution in the presence and absence of AdoDATO (S-adenosyl-1,8-diamino-3-thiooctane), a compound containing both substrate and product moieties. This, the first structure of an aminopropyltransferase, reveals deep cavities for binding substrate and cofactor, and a loop that envelops the active site. The AdoDATO binding site is lined with residues conserved in PAPT enzymes from bacteria to humans, suggesting a universal catalytic mechanism. Other conserved residues act sterically to provide a structural basis for polyamine specificity. The enzyme is tetrameric; each monomer consists of a C-terminal domain with a Rossmann-like fold and an N-terminal beta-stranded domain. The tetramer is assembled using a novel barrel-type oligomerization motif.


    Organizational Affiliation

    Biosciences Division and Structural Biology Center, Argonne National Laboratory, 9700 South Cass Ave., Bldg. 202, Argonne, Illinois 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spermidine synthase
A, B, C, D
296Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: speE
EC: 2.5.1.16
Find proteins for Q9WZC2 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WZC2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AAT
Query on AAT

Download SDF File 
Download CCD File 
A, C, D
S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE
C18 H29 N7 O3 S
SUUGLGYBZXSJAA-SCFUHWHPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AATIC50: 200 nM BINDINGMOAD
AATIC50: 200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 132.519α = 90.00
b = 198.020β = 90.00
c = 51.731γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
d*TREKdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance