7JW3

Crystal structure of Aedes aegypti Nibbler NTD domain

Summary for 7JW3

• Entry DOI: 10.2210/pdb7jw3/pdb
• Descriptor: Exonuclease mut-7 homolog (1 entity in total)
• Functional Keywords: nibbler, exoribonuclease, microrna trimming, pirna trimming, heat, rna binding protein
• Biological source: Aedes aegypti (Yellowfever mosquito)
• Total number of polymer chains: 3
• Total formula weight: 136870.88

Authors

Xie, W.,Sowemimo, I.,Hayashi, R.,Wang, J.,Brennecke, J.,Ameres, S.L.,Patel, D.J. (deposition date: 2020-08-24, release date: 2021-01-20, Last modification date: 2024-10-23)

Primary citation

Xie, W.,Sowemimo, I.,Hayashi, R.,Wang, J.,Burkard, T.R.,Brennecke, J.,Ameres, S.L.,Patel, D.J.
Structure-function analysis of microRNA 3'-end trimming by Nibbler.
Proc.Natl.Acad.Sci.USA, 117:30370-30379, 2020

PubMed Abstract: Nibbler (Nbr) is a 3'-to-5' exoribonuclease whose catalytic 3'-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr's N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3'-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Nbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays in S2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain of and Nbr adopt a mixed α/β-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr's EXO domain exhibits Mn-dependent ssRNA-specific 3'-to-5' exoribonuclease activity. Modeling of a 3' terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2'--methylation of the 3'-U would result in a steric clash with a tryptophan side chain, suggesting that 2'--methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.

PubMed: 33199607
DOI: 10.1073/pnas.2018156117

Experimental method

X-RAY DIFFRACTION (3.05 Å)