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TitleA shape-shifting nuclease unravels structured RNA.
Journal, issue, pagesNat Struct Mol Biol, Vol. 30, Issue 3, Page 339-347, Year 2023
Publish dateFeb 23, 2023
AuthorsKatarina Meze / Armend Axhemi / Dennis R Thomas / Ahmet Doymaz / Leemor Joshua-Tor /
PubMed AbstractRNA turnover pathways ensure appropriate gene expression levels by eliminating unwanted transcripts. Dis3-like 2 (Dis3L2) is a 3'-5' exoribonuclease that plays a critical role in human development. ...RNA turnover pathways ensure appropriate gene expression levels by eliminating unwanted transcripts. Dis3-like 2 (Dis3L2) is a 3'-5' exoribonuclease that plays a critical role in human development. Dis3L2 independently degrades structured substrates, including coding and noncoding 3' uridylated RNAs. While the basis for Dis3L2's substrate recognition has been well characterized, the mechanism of structured RNA degradation by this family of enzymes is unknown. We characterized the discrete steps of the degradation cycle by determining cryogenic electron microscopy structures representing snapshots along the RNA turnover pathway and measuring kinetic parameters for RNA processing. We discovered a dramatic conformational change that is triggered by double-stranded RNA (dsRNA), repositioning two cold shock domains by 70 Å. This movement exposes a trihelix linker region, which acts as a wedge to separate the two RNA strands. Furthermore, we show that the trihelix linker is critical for dsRNA, but not single-stranded RNA, degradation. These findings reveal the conformational plasticity of Dis3L2 and detail a mechanism of structured RNA degradation.
External linksNat Struct Mol Biol / PubMed:36823385 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 5.9 Å
Structure data

27827

8e27

EMDB-27827, PDB-8e27:
RNA-free Human Dis3L2
Method: EM (single particle) / Resolution: 3.4 Å

27828

8e28

EMDB-27828, PDB-8e28:
Human Dis3L2 in complex with hairpin A-GCU14
Method: EM (single particle) / Resolution: 3.1 Å

27829

8e29

EMDB-27829: Human Dis3L2 in complex with hairpinC-U12
PDB-8e29: Human Dis3L2 in complex with hairpin C-U12
Method: EM (single particle) / Resolution: 3.1 Å

27830

8e2a

EMDB-27830, PDB-8e2a:
Human Dis3L2 in complex with hairpin D-U7
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-27831: Wild-type HsDis3L2 in complex with 50% GC hairpin E-U7
Method: EM (single particle) / Resolution: 5.9 Å

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsRNA BINDING PROTEIN/RNA / 3'-5' exonuclease / RNA-free exonuclease / human exonuclease / RNA BIND PROTEIN-RNA complex / RNA BINDING PROTEIN-RNA complex / ds-RNA bound exonuclease

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