1,028
Views
1
CrossRef citations to date
0
Altmetric
Research Paper

Structural basis for Dicer-like function of an engineered RNase III variant and insights into the reaction trajectory of two-Mg2+-ion catalysis

ORCID Icon, ORCID Icon & ORCID Icon
Pages 908-915 | Received 09 May 2022, Accepted 05 Jul 2022, Published online: 13 Jul 2022

References

  • Robertson HD, Webster RE, Zinder ND. Purification and properties of ribonuclease III from Escherichia coli. J Biol Chem. 1968;243:82–91.
  • Nicholson AW. RNAi: a guide to gene silencing. Hannon GJ, ed. New York: Cold Spring Harbor Laboratory Press, Cold Spring Harbor; 2003. p. 149–174.
  • Svoboda P, Di Cara A. Hairpin RNA: a secondary structure of primary importance. Cell Mol Life Sci. 2006;63:901–908.
  • Court DL, Belasco JG, Brawerman G, editors. Control of messenger RNA stability. RNA processing and degradation by RNase III. New York: Academic Press; 1993. p. 71–116.
  • Liu Z, Wang J, Cheng H, et al. Cryo-EM structure of human Dicer and its complexes with a pre-miRNA Substrate. Cell. 2018;173:1191–1203 e1112.
  • Gan J, Tropea JE, Austin BP, et al. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell. 2006;124:355–366.
  • Jin L, Song H, Tropea JE, et al. The molecular mechanism of dsRNA processing by a bacterial Dicer. Nucleic Acids Res. 2019;47:4707–4720.
  • Weinberg DE, Nakanishi K, Patel DJ, et al. The inside-out mechanism of Dicers from budding yeasts. Cell. 2011;146:262–276.
  • Yang D, Buchholz F, Huang Z, et al. Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc Natl Acad Sci USA. 2002;99:9942–9947.
  • Nicholson AW. Ribonuclease III mechanisms of double-stranded RNA cleavage. Wiley interdisciplinary reviews. RNA. 2014;5:31–48.
  • Court DL, Gan J, Liang Y-H, et al. RNase III: genetics and function; structure and mechanism. Annu Rev Genet. 2013;47:405–431.
  • Gan J, Shaw G, Tropea JE, et al. A stepwise model for double-stranded RNA processing by ribonuclease III. Mol Microbiol. 2008;67:143–154.
  • Gan J, Tropea JE, Austin BP, et al. Intermediate states of ribonuclease III in complex with double-stranded RNA. Structure (Camb). 2005;13:1435–1442.
  • Xiao J, Feehery CE, Tzertzinis G, et al. E. coli RNase III(E38A) generates discrete-sized products from long dsRNA. RNA. 2009;15:984–991.
  • Yang W, Lee JY, Nowotny M. Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol Cell. 2006;22:5–13.
  • Liang YH, Lavoie M, Comeau MA, et al. Structure of a eukaryotic RNase III postcleavage complex reveals a double-ruler mechanism for substrate selection. Mol Cell. 2014;54:431–444.
  • Blaszczyk J, Tropea JE, Bubunenko M, et al. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure. 2001;9:1225–1236.
  • Zamore PD. Thirty-three years later, a glimpse at the ribonuclease III active site. Mol Cell. 2001;8:1158–1160.
  • Mantina M, Chamberlin AC, Valero R, et al. Consistent van der Waals radii for the whole main group. J Phys Chem A. 2009;113:5806–5812.
  • Nowotny M, Yang W. Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. EMBO J. 2006;25:1924–1933.
  • Batra VK, Beard WA, Shock DD, et al. Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure. 2006;14:757–766.
  • Kapust RB, Tözsér J, Fox JD, et al., Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. 2001;Protein Eng. 14:993–1000.
  • Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–326.
  • McCoy AJ, Grosse-Kunstleve RW, Adams PD, et al. Phaser crystallographic software. J Appl Crystallogr. 2007;40:658–674.
  • Terwilliger TC, Dimaio F, Read RJ, et al. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J Struct Funct Genomics. 2012;13:81–90.
  • Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. 2004;Acta Crystallogr D. 60:2126–2132.
  • Chou FC, Sripakdeevong P, Dibrov SM, et al. Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nat Methods. 2013;10:74–76.
  • Sripakdeevong P, Kladwang W, Das R. An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling. Proc Natl Acad Sci USA. 2011;108:20573–20578.
  • Adams PD, Afonine PV, Bunkoczi G, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D. 2010; 66: 213–221.
  • Gore S, Sanz Garcia E, Hendrickx PMS, et al. Validation of structures in the protein data bank. Structure. 2017;25:1916–1927.