Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 136.74 kDa 
• Atom Count: 10234 
• Modelled Residue Count: 1151 
• Deposited Residue Count: 1184 
• Unique protein chains: 1

1INL

Crystal Structure of Spermidine Synthase from Thermotoga Maritima

• PDB DOI: 10.2210/pdb1INL/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-05-14 Released: 2001-11-21 
• Deposition Author(s): Korolev, S., Skarina, T., Ikeguchi, Y., Pegg, A.E., Joachimiak, A., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.213 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

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

• PubMed: 11731804 
• DOI: 10.1038/nsb737
• Primary Citation of Related Structures:  
  1INL, 1JQ3


• 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 1.5 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B, C, D	296	Thermotoga maritima	Mutation(s): 0  EC: 2.5.1.16
UniProt
Find proteins for Q9WZC2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZC2  Go to UniProtKB:  Q9WZC2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.213 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.436	α = 90
b = 197.812	β = 90
c = 51.627	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
HKL-2000	data reduction
SnB	phasing
SOLVE	phasing
DM	model building
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-14 
• Released Date: 2001-11-21 
Deposition Author(s): Korolev, S., Skarina, T., Ikeguchi, Y., Pegg, A.E., Joachimiak, A., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• 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
• Version 1.3: 2014-11-12
  Changes: Structure summary
• Version 1.4: 2017-10-04
  Changes: Refinement description