1JQ3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • R-Value Observed: 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 Biol 9: 27-31

  • DOI: 10.1038/nsb737
  • Primary Citation of Related Structures:  
    1JQ3, 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 been solved to 1 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spermidine synthase ABCD296Thermotoga maritimaMutation(s): 0 
EC: 2.5.1.16
Find proteins for Q9WZC2 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9WZC2 
Go to UniProtKB:  Q9WZC2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AAT
Query on AAT

Download Ideal Coordinates 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  PDBBind
AATIC50:  200   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.519α = 90
b = 198.02β = 90
c = 51.731γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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