Crystal Structure of Spermidine Acetyltransferase from Escherichia coli

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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Molecular mechanism underlying promiscuous polyamine recognition by spermidine acetyltransferase

Sugiyama, S.Ishikawa, S.Tomitori, H.Niiyama, M.Hirose, M.Miyazaki, Y.Higashi, K.Murata, M.Adachi, H.Takano, K.Murakami, S.Inoue, T.Mori, Y.Kashiwagi, K.Igarashi, K.Matsumura, H.

(2016) Int J Biochem Cell Biol 76: 87-97

  • DOI: https://doi.org/10.1016/j.biocel.2016.05.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Spermidine acetyltransferase (SAT) from Escherichia coli, which catalyses the transfer of acetyl groups from acetyl-CoA to spermidine, is a key enzyme in controlling polyamine levels in prokaryotic cells. In this study, we determined the crystal structure of SAT in complex with spermidine (SPD) and CoA at 2.5Å resolution. SAT is a dodecamer organized as a hexamer of dimers. The secondary structural element and folding topology of the SAT dimer resemble those of spermidine/spermine N(1)-acetyltransferase (SSAT), suggesting an evolutionary link between SAT and SSAT. However, the polyamine specificity of SAT is distinct from that of SSAT and is promiscuous. The SPD molecule is also located at the inter-dimer interface. The distance between SPD and CoA molecules is 13Å. A deep, highly acidic, water-filled cavity encompasses the SPD and CoA binding sites. Structure-based mutagenesis and in-vitro assays identified SPD-bound residues, and the acidic residues lining the walls of the cavity are mostly essential for enzymatic activities. Based on mutagenesis and structural data, we propose an acetylation mechanism underlying promiscuous polyamine recognition for SAT.

  • Organizational Affiliation

    Graduate School of Science, Osaka University, Suita, Osaka 565-0871, Japan; JST, ERATO, Lipid Active Structure Project, Osaka 565-0871, Japan. Electronic address: sugiyama@cryst.eei.eng.osaka-u.ac.jp.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine N1-acetyltransferaseA,
B [auth C],
C [auth B],
170Escherichia coli LY180Mutation(s): 0 
Find proteins for A0A0M3KKU5 (Escherichia coli LY180)
Explore A0A0M3KKU5 
Go to UniProtKB:  A0A0M3KKU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KKU5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.688α = 90
b = 148.688β = 90
c = 148.688γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations