4JLY

Dodecameric structure of spermidine N-acetyltransferase from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.882 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG.

Filippova, E.V.Weigand, S.Osipiuk, J.Kiryukhina, O.Joachimiak, A.Anderson, W.F.

(2015) J.Mol.Biol. 427: 3538-3553

  • DOI: 10.1016/j.jmb.2015.09.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The spermidine N-acetyltransferase SpeG is a dodecameric enzyme that catalyzes the transfer of an acetyl group from acetyl coenzyme A to polyamines such as spermidine and spermine. SpeG has an allosteric polyamine-binding site and acetylating polyami ...

    The spermidine N-acetyltransferase SpeG is a dodecameric enzyme that catalyzes the transfer of an acetyl group from acetyl coenzyme A to polyamines such as spermidine and spermine. SpeG has an allosteric polyamine-binding site and acetylating polyamines regulate their intracellular concentrations. The structures of SpeG from Vibrio cholerae in complexes with polyamines and cofactor have been characterized earlier. Here, we present the dodecameric structure of SpeG from V. cholerae in a ligand-free form in three different conformational states: open, intermediate and closed. All structures were crystallized in C2 space group symmetry and contain six monomers in the asymmetric unit cell. Two hexamers related by crystallographic 2-fold symmetry form the SpeG dodecamer. The open and intermediate states have a unique open dodecameric ring. This SpeG dodecamer is asymmetric except for the one 2-fold axis and is unlike any known dodecameric structure. Using a fluorescence thermal shift assay, size-exclusion chromatography with multi-angle light scattering, small-angle X-ray scattering analysis, negative-stain electron microscopy and structural analysis, we demonstrate that this unique open dodecameric state exists in solution. Our combined results indicate that polyamines trigger conformational changes and induce the symmetric closed dodecameric state of the protein when they bind to their allosteric sites.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spermidine n1-acetyltransferase
A, B, C, D, E, F
176Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: speG
EC: 2.3.1.57
Find proteins for Q9KL03 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KL03
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 194.860α = 90.00
b = 71.771β = 134.53
c = 136.728γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
PHENIXmodel building
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Database references
  • Version 1.2: 2015-11-18
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description