Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine

Abstract

The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.

Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly

“…Drg1 performs this function as a single protein. A recent study characterized the cryo-EM structure of Drg1 and suggested potential homology between this protein and SPATA5 ( Prattes et al, 2021 ).…”

Ribosome-Directed Therapies in Cancer

“…On the NIH clinical collection website, 446 small molecules have been registered that have already been used in clinical studies ( ) [ 61 ]. The drug diazaborine has been shown to bind with Drg1 and specifically block ATP hydrolysis, preventing Rlp24 release from pre-60S particles [ 62 , 63 ].…”

Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1

“… 16 ). The D2-domain-specific Drg1 inhibitor diazaborine therefore blocks Rlp24 extraction and prevents cell growth and proliferation 16 , 17 . The mechanism of Rlp24 release by Drg1 was unknown.…”