Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with CoA and spermine

Experimental Data Snapshot

  • Resolution: 2.61 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure.

Filippova, E.V.Kuhn, M.L.Osipiuk, J.Kiryukhina, O.Joachimiak, A.Ballicora, M.A.Anderson, W.F.

(2015) J Mol Biol 427: 1316-1334

  • DOI: https://doi.org/10.1016/j.jmb.2015.01.009
  • Primary Citation of Related Structures:  
    4JJX, 4MHD, 4MI4, 4NCZ, 4R57, 4R87

  • PubMed Abstract: 

    Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis.

  • Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine n1-acetyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
176Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_A0947
Find proteins for Q9KL03 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KL03 
Go to UniProtKB:  Q9KL03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KL03
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on COA

Download Ideal Coordinates CCD File 
BA [auth J]
DA [auth K]
FA [auth L]
M [auth A]
N [auth B]
BA [auth J],
DA [auth K],
FA [auth L],
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
S [auth F],
T [auth G],
V [auth H],
Y [auth I]
C21 H36 N7 O16 P3 S
Query on SPM

Download Ideal Coordinates CCD File 
CA [auth J]
EA [auth K]
R [auth E]
U [auth G]
W [auth H]
CA [auth J],
EA [auth K],
R [auth E],
U [auth G],
W [auth H],
Z [auth I]
C10 H26 N4
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth I],
GA [auth L],
X [auth H]
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.61 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 3
  • Diffraction Data: https://doi.org/10.18430/M34R87
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.948α = 90
b = 176.948β = 90
c = 67.009γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description