publication . Article . Other literature type . 2016

Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.

Dinshaw J. Patel; Jennifer Gebetsberger; Aiming Ren; Aiming Ren; Michael Andreas Juen; Christoph Kreutz; Ronald Micura; Nikola Vušurović; Pu Gao;
Open Access English
  • Published: 11 Jul 2016 Journal: Nature chemical biology, volume 12, issue 9, pages 702-708 (issn: 1552-4450, eissn: 1552-4469, Copyright policy)
Abstract
The field of small self-cleaving nucleolytic ribozymes has been invigorated by the recent discovery of the twister, twister-sister, pistol and hatchet ribozymes. We report the crystal structure of a pistol ribozyme termed env25, which adopts a compact tertiary architecture stabilized by an embedded pseudoknot fold. The G-U cleavage site adopts a splayed-apart conformation with in-line alignment of the modeled 2'-O of G for attack on the adjacent to-be-cleaved P-O5' bond. Highly conserved residues G40 (N1 position) and A32 (N3 and 2'-OH positions) are aligned to act as a general base and a general acid, respectively, to accelerate cleavage chemistry, with their r...
Subjects
free text keywords: Article, Cell Biology, Molecular Biology, Stereochemistry, Pseudoknot, Cleavage (embryo), Nuclear magnetic resonance spectroscopy, RNA, VS ribozyme, Mammalian CPEB3 ribozyme, Ribozyme, biology.protein, biology, Chemistry, Hairpin ribozyme
Funded by
FWF| Chemical synthesis of modified twister ribozymes
Project
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: P 27947
  • Funding stream: Einzelprojekte
,
NIH| Biochemical and structural characterization of RNA turnover processes and resolu
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U19CA179564-02
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| NE-CAT Center for Advanced Macromolecular Crystallography
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 4P41GM103403-14
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
FWF| Single-molecule FRET investigations of riboswitch-mediated translational control
Project
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: I 1040
  • Funding stream: Internationale Projekte
,
FWF| Seeing the invisible – RNA excited state structures
Project
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: P 28725
  • Funding stream: Einzelprojekte
44 references, page 1 of 3

Jimenez, RM, Polanco, JA, Luptak, A. Chemistry and Biology of Self-Cleaving Ribozymes. Trends Biochem Sci. 2015; 40: 648-61 [OpenAIRE] [PubMed]

Weinberg, Z. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nat Chem Biol. 2015; 11: 606-10 [OpenAIRE] [PubMed]

Prody, GA, Bakos, JT, Buzayan, JM, Schneider, IR, Bruening, G. Autolytic processing of dimeric plant virus satellite RNA. Science. 1986; 231: 1577-80 [OpenAIRE] [PubMed]

Hutchins, CJ, Rathjen, PD, Forster, AC, Symons, RH. Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Res. 1986; 14: 3627-40 [OpenAIRE] [PubMed]

Saville, BJ, Collins, RA. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell. 1990; 61: 685-96 [OpenAIRE] [PubMed]

Perreault, J. Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol. 2011; 7: e1002031 [OpenAIRE] [PubMed]

Webb, CH, Riccitelli, NJ, Ruminski, DJ, Luptak, A. Widespread occurrence of self-cleaving ribozymes. Science. 2009; 326: 953 [OpenAIRE] [PubMed]

Buzayan, JM, Gerlach, WL, Bruening, G. Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature. 1986; 323: 349-353 [OpenAIRE]

Fedor, MJ. Structure and function of the hairpin ribozyme. J Mol Biol. 2000; 297: 269-91 [OpenAIRE] [PubMed]

Winkler, WC, Nahvi, A, Roth, A, Collins, JA, Breaker, RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature. 2004; 428: 281-6 [OpenAIRE] [PubMed]

Watson, PY, Fedor, MJ. The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis. Nat Chem Biol. 2012; 8: 963-5 [OpenAIRE] [PubMed]

Webb, CH, Luptak, A. HDV-like self-cleaving ribozymes. RNA Biol. 2011; 8: 719-27 [OpenAIRE] [PubMed]

Lilley, DM. The Varkud satellite ribozyme. Rna. 2004; 10: 151-8 [OpenAIRE] [PubMed]

Martick, M, Scott, WG. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell. 2006; 126: 309-20 [OpenAIRE] [PubMed]

Rupert, PB, Ferre-D'Amare, AR. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature. 2001; 410: 780-6 [PubMed]

44 references, page 1 of 3
Abstract
The field of small self-cleaving nucleolytic ribozymes has been invigorated by the recent discovery of the twister, twister-sister, pistol and hatchet ribozymes. We report the crystal structure of a pistol ribozyme termed env25, which adopts a compact tertiary architecture stabilized by an embedded pseudoknot fold. The G-U cleavage site adopts a splayed-apart conformation with in-line alignment of the modeled 2'-O of G for attack on the adjacent to-be-cleaved P-O5' bond. Highly conserved residues G40 (N1 position) and A32 (N3 and 2'-OH positions) are aligned to act as a general base and a general acid, respectively, to accelerate cleavage chemistry, with their r...
Subjects
free text keywords: Article, Cell Biology, Molecular Biology, Stereochemistry, Pseudoknot, Cleavage (embryo), Nuclear magnetic resonance spectroscopy, RNA, VS ribozyme, Mammalian CPEB3 ribozyme, Ribozyme, biology.protein, biology, Chemistry, Hairpin ribozyme
Funded by
FWF| Chemical synthesis of modified twister ribozymes
Project
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: P 27947
  • Funding stream: Einzelprojekte
,
NIH| Biochemical and structural characterization of RNA turnover processes and resolu
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U19CA179564-02
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| NE-CAT Center for Advanced Macromolecular Crystallography
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 4P41GM103403-14
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
FWF| Single-molecule FRET investigations of riboswitch-mediated translational control
Project
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: I 1040
  • Funding stream: Internationale Projekte
,
FWF| Seeing the invisible – RNA excited state structures
Project
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: P 28725
  • Funding stream: Einzelprojekte
44 references, page 1 of 3

Jimenez, RM, Polanco, JA, Luptak, A. Chemistry and Biology of Self-Cleaving Ribozymes. Trends Biochem Sci. 2015; 40: 648-61 [OpenAIRE] [PubMed]

Weinberg, Z. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nat Chem Biol. 2015; 11: 606-10 [OpenAIRE] [PubMed]

Prody, GA, Bakos, JT, Buzayan, JM, Schneider, IR, Bruening, G. Autolytic processing of dimeric plant virus satellite RNA. Science. 1986; 231: 1577-80 [OpenAIRE] [PubMed]

Hutchins, CJ, Rathjen, PD, Forster, AC, Symons, RH. Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Res. 1986; 14: 3627-40 [OpenAIRE] [PubMed]

Saville, BJ, Collins, RA. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell. 1990; 61: 685-96 [OpenAIRE] [PubMed]

Perreault, J. Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol. 2011; 7: e1002031 [OpenAIRE] [PubMed]

Webb, CH, Riccitelli, NJ, Ruminski, DJ, Luptak, A. Widespread occurrence of self-cleaving ribozymes. Science. 2009; 326: 953 [OpenAIRE] [PubMed]

Buzayan, JM, Gerlach, WL, Bruening, G. Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature. 1986; 323: 349-353 [OpenAIRE]

Fedor, MJ. Structure and function of the hairpin ribozyme. J Mol Biol. 2000; 297: 269-91 [OpenAIRE] [PubMed]

Winkler, WC, Nahvi, A, Roth, A, Collins, JA, Breaker, RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature. 2004; 428: 281-6 [OpenAIRE] [PubMed]

Watson, PY, Fedor, MJ. The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis. Nat Chem Biol. 2012; 8: 963-5 [OpenAIRE] [PubMed]

Webb, CH, Luptak, A. HDV-like self-cleaving ribozymes. RNA Biol. 2011; 8: 719-27 [OpenAIRE] [PubMed]

Lilley, DM. The Varkud satellite ribozyme. Rna. 2004; 10: 151-8 [OpenAIRE] [PubMed]

Martick, M, Scott, WG. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell. 2006; 126: 309-20 [OpenAIRE] [PubMed]

Rupert, PB, Ferre-D'Amare, AR. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature. 2001; 410: 780-6 [PubMed]

44 references, page 1 of 3
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