3WR7

Crystal Structure of Spermidine Acetyltransferase from Escherichia coli

Summary for 3WR7

• Entry DOI: 10.2210/pdb3wr7/pdb
• Descriptor: Spermidine N1-acetyltransferase, SPERMIDINE, COENZYME A, ... (4 entities in total)
• Functional Keywords: alpha and beta, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 84835.68

Authors

Sugiyama, S.,Ishikawa, S.,Tomitori, S.,Niiyama, M.,Hirose, M.,Miyazaki, Y.,Higashi, K.,Adachi, H.,Takano, K.,Murakami, S.,Inoue, T.,Mori, Y.,Kashiwagi, K.,Igarashi, K.,Matsumura, H. (deposition date: 2014-02-20, release date: 2015-09-02, Last modification date: 2024-03-20)

Primary citation

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.
Molecular mechanism underlying promiscuous polyamine recognition by spermidine acetyltransferase
Int.J.Biochem.Cell Biol., 76:87-97, 2016

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.

PubMed: 27163532
DOI: 10.1016/j.biocel.2016.05.003

Experimental method

X-RAY DIFFRACTION (2.5 Å)