Minimal hammerhead ribozymes with uncompromised catalytic activity

Journal of Molecular Biology

Volumn 427, Issue 14, 2015, Pages 2340-2347

  O'Rourke, Sara M ^a   Estell, William ^a   Scott, William G ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Hammerhead ribozyme; Ribozyme kinetics; Rna catalysis; Rna structure; Rna tertiary contacts

Indexed keywords

HAMMERHEAD RIBOZYME; NUCLEOPHILE; NUCLEOTIDE; RIBOZYME;

ARTICLE; BASE PAIRING; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME KINETICS; IN VIVO STUDY; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN SECONDARY STRUCTURE; RNA CLEAVAGE; RNA SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; HUMAN; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; X RAY CRYSTALLOGRAPHY;

SPHYRNA;

BASE PAIRING; BASE SEQUENCE; CATALYSIS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC;

EID: 84934989383     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2015.05.005     Document Type: Article

References (26)

1. Prody GA, Bakos JT, Buzayan JM, Schneider IR, Breuning G. Autolytic processing of dimeric plant virus satellite RNA. Science 1986;231:1577-80.
2. Forster AC, Symons RH. Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell 1987;50:9-16.
3. Martick M, Horan LH, Noller HF, Scott WG. A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. Nature 2008;454:899-902.
4. García-Robles I, Sánchez-Navarro J, de la Peña M. Intronic hammerhead ribozymes in mRNA biogenesis. Biol Chem 2012;393:1317-26.
5. Uhlenbeck OC. A small catalytic oligoribonucleotide. Nature 1987;328:596-600.
6. Wedekind JE, McKay DB. Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis. Annu Rev Biophys Biomol Struct 1998;27:475-502.
7. Anderson M, Schultz EP, Martick M, Scott WG. Active-site monovalent cations revealed in a 1.55-Å-resolution hammerhead ribozyme structure. J Mol Biol 2013;425:3790-8.
8. Hammann C, Luptak A, Perreault J, de la Peña M. The ubiquitous hammerhead ribozyme. RNA 2012;18:871-85.
9. Ferré-D'Amaré AR, Scott WG. Small self-cleaving ribozymes. Cold Spring Harb Perspect Biol 2010;2:a003574.
10. Ruffner DE, Stormo GD, Uhlenbeck OC. Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 1990;29:10695-702.
11. Hertel KJ, Herschlag D, Uhlenbeck OC. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry 1994;33:3374-85.
12. Stage-Zimmermann TK, Uhlenbeck OC. Hammerhead ribozyme kinetics. RNA 1998;4:875-89.
13. De la Peña M, Gago S, Flores R. Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J 2003;22:5561-70.
14. Khvorova A, Lescoute A, Westhof E, Jayasena SD. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 2003;10:708-12.
15. Canny MD, Jucker FM, Kellogg E, Khvorova A, Jayasena SD, Pardi A. Fast cleavage kinetics of a natural hammerhead ribozyme. J Am Chem Soc 2004;126:10848-9.
16. Martick M, Scott WG. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 2006;126:309-20.
17. Chi Y-I, Martick M, Lares M, Kim R, Scott WG, Kim S-H. Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol 2008;6:e234.
18. Przybilski R, Hammann C. The hammerhead ribozyme structure brought in line. Chembiochem 2006;7:1641-4.
19. Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, et al. The RNA WikiProject: community annotation of RNA families. RNA 2008;14:1-3.
20. Ferbeyre G, Smith JM, Cedergren R. Schistosome satellite DNA encodes active hammerhead ribozymes. Mol Cell Biol 1998;18:3880-8.
21. Seehafer C, Kalweit A, Steger G, Gräf S, Hammann C. From alpaca to zebrafish: hammerhead ribozymes wherever you look. RNA 2011;17:21-6.
22. Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA 2001;7:499-512.
23. Jimenez RM, Delwart E, Lupták Andrej. Structure-based search reveals hammerhead ribozymes in the human microbiome. J Biol Chem 2011;286:7737-43.
24. Nelson JA, Shepotinovskaya I, Uhlenbeck OC. Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants. Biochemistry 2005;44:14577-85.
25. Pley HW, Flaherty KM, McKay DB. Three-dimensional structure of a hammerhead ribozyme. Nature 1994;372:68-74.
26. Hertel KJ, Pardi A, Uhlenbeck OC, Koizumi M, Ohtsuka E, Uesugi S, et al. Numbering system for the hammerhead. Nucleic Acids Res 1992;20:3252.