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...
Read more
doi: 10.1038/nchembio.2125
pmc: PMC4990474
pmid: 27398999
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
Related Organizations
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Funded by
FWF| Chemical synthesis of modified twister ribozymes
Project
Chemical synthesis of modified twister ribozymes
  • 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
Biochemical and structural characterization of RNA turnover processes and resolu
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U19CA179564-02
  • Funding stream: NATIONAL CANCER INSTITUTE
, NIH| NE-CAT Center for Advanced Macromolecular Crystallography
Project
NE-CAT Center for Advanced Macromolecular Crystallography
  • 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
Single-molecule FRET investigations of riboswitch-mediated translational control
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: I 1040
  • Funding stream: Internationale Projekte
, FWF| Seeing the invisible – RNA excited state structures
Project
Seeing the invisible – RNA excited state structures
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: P 28725
  • Funding stream: Einzelprojekte
View more
Download fromView all 4 versions
Europe PubMed Central
Article . 2016
Provider: PubMed Central
Nature Chemical Biology
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http://dx.doi.org/10.1038/nche...
Article . 2016
Provider: SNSF P3 Database
http://dx.doi.org/10.1038/nche...
Other literature type . 2016
Provider: Datacite
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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...
Read more
doi: 10.1038/nchembio.2125
pmc: PMC4990474
pmid: 27398999
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
Related Organizations
View more
Funded by
FWF| Chemical synthesis of modified twister ribozymes
Project
Chemical synthesis of modified twister ribozymes
  • 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
Biochemical and structural characterization of RNA turnover processes and resolu
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U19CA179564-02
  • Funding stream: NATIONAL CANCER INSTITUTE
, NIH| NE-CAT Center for Advanced Macromolecular Crystallography
Project
NE-CAT Center for Advanced Macromolecular Crystallography
  • 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
Single-molecule FRET investigations of riboswitch-mediated translational control
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: I 1040
  • Funding stream: Internationale Projekte
, FWF| Seeing the invisible – RNA excited state structures
Project
Seeing the invisible – RNA excited state structures
  • Funder: Austrian Science Fund (FWF) (FWF)
  • Project Code: P 28725
  • Funding stream: Einzelprojekte
View more
Download fromView all 4 versions
Europe PubMed Central
Article . 2016
Provider: PubMed Central
Nature Chemical Biology
Article
Provider: UnpayWall
http://dx.doi.org/10.1038/nche...
Article . 2016
Provider: SNSF P3 Database
http://dx.doi.org/10.1038/nche...
Other literature type . 2016
Provider: Datacite
View more
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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