3WR7

Crystal Structure of Spermidine Acetyltransferase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1016/j.biocel.2016.05.003
  • Primary Citation of Related Structures:  
    3WR7

  • 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 stru ...

    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

    SOSHO Inc., Suita, Osaka 565-0871, Japan; Department of Biotechnology, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan. Electronic address: h-matsu@fc.ritsumei.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spermidine N1-acetyltransferaseABCD170Escherichia coli LY180Mutation(s): 0 
Find proteins for A0A0M3KKU5 (Escherichia coli LY180)
Explore A0A0M3KKU5 
Go to UniProtKB:  A0A0M3KKU5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download CCD File 
A, B, C, D
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
SPD
Query on SPD

Download CCD File 
A, B, C, D
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references