3WR7

Crystal Structure of Spermidine Acetyltransferase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 

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

  • 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

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spermidine N1-acetyltransferase
A, C, B, D
170Escherichia coli LY180Mutation(s): 0 
Find proteins for A0A0M3KKU5 (Escherichia coli LY180)
Go to UniProtKB:  A0A0M3KKU5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
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 SDF File 
Download CCD File 
A, B, C, D
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • Space Group: P 2 3
Unit Cell:
Length (Å)Angle (°)
a = 148.688α = 90.00
b = 148.688β = 90.00
c = 148.688γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
ADSCdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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