3ANX

Crystal structure of triamine/agmatine aminopropyltransferase (SPEE) from thermus thermophilus, complexed with MTA

Summary for 3ANX

• Entry DOI: 10.2210/pdb3anx/pdb
• Descriptor: spermidine synthase, 5'-DEOXY-5'-METHYLTHIOADENOSINE (3 entities in total)
• Functional Keywords: spee, spermine synthase, spermidine synthase, polyamine, spermidine biosynthesis, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Thermus thermophilus
• Total number of polymer chains: 2
• Total formula weight: 72707.14

Authors

Ganbe, T.,Ohnuma, M.,Sato, T.,Tanaka, N.,Oshima, T.,Kumasaka, T. (deposition date: 2010-09-14, release date: 2011-04-13, Last modification date: 2023-11-01)

Primary citation

Ohnuma, M.,Ganbe, T.,Terui, Y.,Niitsu, M.,Sato, T.,Tanaka, N.,Tamakoshi, M.,Samejima, K.,Kumasaka, T.,Oshima, T.
Crystal structures and enzymatic properties of a triamine/agmatine aminopropyltransferase from Thermus thermophilus
J.Mol.Biol., 408:971-986, 2011

PubMed Abstract: To maintain functional conformations of DNA and RNA in high-temperature environments, an extremely thermophilic bacterium, Thermus thermophilus, employs a unique polyamine biosynthetic pathway and produces more than 16 types of polyamines. In the thermophile genome, only one spermidine synthase homolog (SpeE) was found and it was shown to be a key enzyme in the pathway. The catalytic assay of the purified enzyme revealed that it utilizes triamines (norspermidine and spermidine) and agmatine as acceptors in its aminopropyl transfer reaction; therefore, the enzyme was denoted as a triamine/agmatine aminopropyltransferase (TAAPT). We determined the crystal structures of the enzyme complexed with and without the aminopropyl group donor S-adenosylmethionine. Despite sequence and structural similarity with spermidine synthases from other organisms, a novel C-terminal β-sheet and differences in the catalytic site were observed. The C-terminal module interacts with the gatekeeping loop and fixes the open conformation of the loop to recognize larger polyamine substrates such as agmatine and spermidine. Additional computational docking studies suggest that the structural differences of the catalytic site also contribute to recognition of the aminopropyl/aminobutyl or guanidium moiety of the substrates of TAAPT. These results explain in part the extraordinarily diverse polyamine spectrum found in T. thermophilus.

PubMed: 21458463
DOI: 10.1016/j.jmb.2011.03.025

Experimental method

X-RAY DIFFRACTION (2.5 Å)