Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase

Abstract

DNMDP and related compounds, or velcrins, induce complex formation between the phosphodiesterase PDE3A and the SLFN12 protein, leading to a cytotoxic response in cancer cells that express elevated levels of both proteins. The mechanisms by which velcrins induce complex formation, and how the PDE3A-SLFN12 complex causes cancer cell death, are not fully understood. Here, we show that PDE3A and SLFN12 form a heterotetramer stabilized by binding of DNMDP. Interactions between the C-terminal alpha helix of SLFN12 and residues near the active site of PDE3A are required for complex formation, and are further stabilized by interactions between SLFN12 and DNMDP. Moreover, we demonstrate that SLFN12 is an RNase, that PDE3A binding increases SLFN12 RNase activity, and that SLFN12 RNase activity is required for DNMDP response. This new mechanistic understanding will facilitate development of velcrin compounds into new cancer therapies.

Precision Oncology with Drugs Targeting the Replication Stress, ATR, and Schlafen 11

“…Moreover, SLFN11 activity is not limited to the nucleus [ 133 , 134 , 135 , 137 , 147 ] and it remains to be determined whether cytosolic IHC staining of SLFN11 should be taken into consideration [ 141 , 148 ]. This is particularly relevant to the fact that human SLFN proteins including SLFN5, 11, 12, 12L, 13, and 14 have strong similarity in their amino acid sequence ( Figure 6 B) [ 11 , 149 ] and that some of these SLFN proteins only act in the cytosol [ 149 , 150 ]. Hence, careful examination of the epitopes is important for assessing the specificity of SLFN11 antibodies.…”

Structural and biochemical characterization of human Schlafen 5

“…C-terminally truncated rabbit and human SLFN14 (residues 1–400) were shown to bind ribosomes and cleave rRNA ( 43 , 44 ). Other studies showed cleavage of tRNA and rRNA by rat Slfn13 (rSlfn13), human SLFN13, mouse mSlfn8 and human SLFN12, suggesting a role in translational regulation ( 42 , 45 ). Recently, Garvie et al.…”

“…Recently, Garvie et al. presented that a tetrameric complex of two phosphodiesterases PDE3A and two SLFN12 molecules lead to a cytotoxic response in cancer cells ( 45 ). The small molecule DNMDP stabilized binding to PDE3A and increased the RNase activity of SLFN12, which was important for its cytotoxic function.…”

Schlafens: Emerging Proteins in Cancer Cell Biology

“…SLFN12 is stabilized by interaction with Phosphodiesterase 3A (PDE3A) and is recruited and binds the ribosomes to exclude signal recognition peptides and subsequently inhibits translation [ 83 ]. In addition to these effects, SLFN12 has recently been identified as an RNAse that digests ribosomal RNA [ 84 ].…”