Ministry of Education, Youth and Sports of the Czech Republic
LM2018127
チェコ
引用
ジャーナル: Mol Cell / 年: 2022 タイトル: Structural and functional basis of mammalian microRNA biogenesis by Dicer. 著者: David Zapletal / Eliska Taborska / Josef Pasulka / Radek Malik / Karel Kubicek / Martina Zanova / Christian Much / Marek Sebesta / Valeria Buccheri / Filip Horvat / Irena Jenickova / Michaela ...著者: David Zapletal / Eliska Taborska / Josef Pasulka / Radek Malik / Karel Kubicek / Martina Zanova / Christian Much / Marek Sebesta / Valeria Buccheri / Filip Horvat / Irena Jenickova / Michaela Prochazkova / Jan Prochazka / Matyas Pinkas / Jiri Novacek / Diego F Joseph / Radislav Sedlacek / Carrie Bernecky / Dónal O'Carroll / Richard Stefl / Petr Svoboda / 要旨: MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is ...MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer's DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer•-miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.
Endoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting was done using Chimera and then Coot's Real Space Refine Zone.
精密化
空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 134.8 当てはまり具合の基準: Ramachandran Plot, Rotamer Analysis, Density Analysis
得られたモデル
PDB-7yym: Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate
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原子モデル構築 2
詳細
PHENIX Real-space refinement was used for flexible fitting.
精密化
空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 134.8 / 当てはまり具合の基準: Correlation coefficient
得られたモデル
PDB-7yym: Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate
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原子モデル構築 3
詳細
ISOLDE was used for flexible fitting with torsion restraints defined for polypeptide and distance restraints for polyribonucleotide chain.
精密化
空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 134.8 当てはまり具合の基準: Ramachandran Plot, Rotamer Analysis, Clash Score
得られたモデル
PDB-7yym: Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate