Binding and inhibition of human spermidine synthase by decarboxylated S-adenosylhomocysteine.

Publication Type:

Journal Article


Protein Sci, Volume 20, Issue 11, p.1836-44 (2011)


Binding Sites, Catalytic Domain, Crystallography, X-Ray, Decarboxylation, Enzyme Inhibitors, Humans, Plasmodium falciparum, Protein Binding, Protein Structure, Tertiary, Putrescine, S-Adenosylhomocysteine, Spermidine, Spermidine Synthase, Thermotoga maritima


<p>Aminopropyltransferases are essential enzymes that form polyamines in eukaryotic and most prokaryotic cells. Spermidine synthase (SpdS) is one of the most well-studied enzymes in this biosynthetic pathway. The enzyme uses decarboxylated S-adenosylmethionine and a short-chain polyamine (putrescine) to make a medium-chain polyamine (spermidine) and 5'-deoxy-5'-methylthioadenosine as a byproduct. Here, we report a new spermidine synthase inhibitor, decarboxylated S-adenosylhomocysteine (dcSAH). The inhibitor was synthesized, and dose-dependent inhibition of human, Thermatoga maritima, and Plasmodium falciparum spermidine synthases, as well as functionally homologous human spermine synthase, was determined. The human SpdS/dcSAH complex structure was determined by X-ray crystallography at 2.0 Å resolution and showed consistent active site positioning and coordination with previously known structures. Isothermal calorimetry binding assays confirmed inhibitor binding to human SpdS with K(d) of 1.1 ± 0.3 μM in the absence of putrescine and 3.2 ± 0.1 μM in the presence of putrescine. These results indicate a potential for further inhibitor development based on the dcSAH scaffold.</p>