Download MendeleyApaH decaps Np 4 N-capped RNAs in two alternative orientations.
Nuthanakanti, A., Korn, M., Levenson-Palmer, R., Wu, Y., Babu, N.R., Huang, X., Banh, R.S., Belasco, J.G., Serganov, A.(2025) Nat Chem Biol
- PubMed: 40789943 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1038/s41589-025-01991-4
- Primary Citation Related Structures:
9OJD, 9OJP, 9OJQ, 9OJW, 9OJX, 9OK1, 9OK2, 9OLN, 9OLY, 9OLZ, 9OM9, 9OMC, 9OMU, 9OMW, 9OMX, 9ON0, 9ON7, 9OND, 9ONG, 9OON, 9OOY, 9OP2, 9OPG, 9OPH, 9OQ9, 9OQB - PubMed Abstract:
Enigmatic dinucleoside tetraphosphates, known as 'alarmones' (Np 4 Ns), have recently been shown to function in bacteria as precursors to Np 4 caps on transcripts, likely influencing RNA longevity and cellular adaptation to stress. In proteobacteria, ApaH is the predominant enzyme that hydrolyzes Np 4 Ns and decaps Np 4 -capped RNAs to initiate their 5'-end-dependent degradation. Here we conducted a biochemical and structural study to uncover the catalytic mechanism of Escherichia coli ApaH, a prototypic symmetric Np 4 N hydrolase, on various Np 4 Ns and Np 4 -capped RNAs. We found that the enzyme uses a unique combination of nonspecific and semispecific substrate recognition, enabling substrates to bind in two orientations with a slight orientational preference. Despite such exceptional recognition properties, ApaH efficiently decaps various Np 4 -capped mRNAs and sRNAs, thereby impacting their lifetimes. Our findings highlight the need to determine substrate orientation preferences before designing substrate-mimicking drugs, as enzymes may escape activity modulation with one of the alternative substrate orientations.
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York City, NY, USA.
Organizational Affiliation:
