Ribozymes

Current Opinion in Structural Biology

Volumn 17, Issue 3, 2007, Pages 280-286

  Scott, William G ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLMS ENZYME; GLUCOSE 6 PHOSPHATE; PEPTIDYLTRANSFERASE; RIBONUCLEASE; RIBONUCLEASE P; RIBOZYME; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; CRYSTAL STRUCTURE; DIELS ALDER REACTION; GEOBACILLUS STEAROTHERMOPHILUS; INTRON; MOLECULAR BIOLOGY; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; REVIEW;

ANIMALS; HUMANS; RIBONUCLEASE P; RNA, CATALYTIC;

EID: 34447092247     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2007.05.003     Document Type: Review

References (29)

1. Nissen P., Hansen J., Ban N., Moore P.B., and Steitz T.A. The structural basis of ribosome activity in peptide bond synthesis. Science 289 (2000) 920-930
2. Steitz T.A., and Moore P.B. RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem Sci 28 (2003) 411-418
3. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., and Cate J.H. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310 (2005) 827-834. The first of the near atomic resolution crystal structures of the entire 70S ribosome and the first crystal structure of the E. coli ribosome. Two crystallographically independent ribosomes are present in the asymmetric unit and appear to represent two different conformational states relevant to translation.
4. Selmer M., Dunham C.M., Murphy IV F.V., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., and Ramakrishnan V. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942. A new crystal form of the T. thermophilus 70S ribosome gives us a 2.8 Å view of a 'batteries-included' version of the ribosome. Intriguingly, the N terminus of a protein is seen about 4 Å from the active site.
5. ••].
6. Steitz T.A., and Steitz J.A. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90 (1993) 6498-6502
7. 2+ ion in solution, in each case five of the water ligands are replaced with oxygen atoms from the RNA.
8. Murray J.B., Seyhan A.A., Walter N.G., Burke J.M., and Scott W.G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol 5 (1998) 587-595
9. Guerrier-Takada C., Gardiner K., Marsh T., Pace N., and Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35 (1983) 849-857
10. ••]).
11. ••]).
12. Marquez S.M., Chen J.L., Evans D., and Pace N.R. Structure and function of eukaryotic ribonuclease P RNA. Mol Cell 24 (2006) 445-456
13. Kruger K., Grabowski P.J., Zaug A.J., Sands J., Gottschling D.E., and Cech T.R. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31 (1982) 147-157
14. Zaug A.J., and Cech T.R. The intervening sequence RNA of Tetrahymena is an enzyme. Science 231 (1986) 470-475
15. Adams P.L., Stahley M.R., Kosek A.B., Wang J., and Strobel S.A. Crystal structure of a self-splicing group I intron with both exons. Nature 430 (2004) 45-50
16. Guo F., Gooding A.R., and Cech T.R. Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol Cell 16 (2004) 351-362
17. Golden B.L., Kim H., and Chase E. Crystal structure of a phage Twort group I ribozyme-product complex. Nat Struct Mol Biol 12 (2005) 82-89. A third species of the group I intron adds a third catalytic state to an expanding gallery of group I intron structures. This phage Twort group I intron is an enzyme-product complex and reveals how phage introns encase the catalytic core within a framework of peripheral structural RNA elements.
18. Vicens Q., and Cech T.R. Atomic level architecture of group I introns revealed. Trends Biochem Sci 31 (2006) 41-51. An excellent and current review of the various group I intron structures now available.
19. Serganov A., Keiper S., Malinina L., Tereshko V., Skripkin E., Hobartner C., Polonskaia A., Phan A.T., Wombacher R., Micura R., et al. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat Struct Mol Biol 12 (2005) 218-224. Although it is not a naturally occurring ribozyme, the Diels-Alder ribozyme is of interest not only because it catalyzes formation of a carbon-carbon bond, but also because it invites comparison to the structure of a catalytic antibody evolved to catalyze the same reaction. Hence, the Diels-Alder ribozyme permits us to compare RNA and protein in vitro evolution in three dimensions.
20. Klein D.J., and Ferre-D'Amare A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313 (2006) 1752-1756. The structure of the glmS ribozyme is unique for two reasons. Not only is it a riboswitch, but also the switch, which corresponds to the binding of GlcN6P, provides the acidic component of acid-base catalysis in this ribozyme.
21. Cochrane J.C., Lipchock S.V., and Strobel S.A. Structural investigation of the glmS ribozyme bound to its catalytic cofactor. Chem Biol 14 (2006) 97-105. A second glmS structure shows that GlcN6P binds to the ribozyme in the same way that the competitive inhibitor Gly6P does. It reveals additional small changes in the active site that may be relevant to catalysis and confirms that this ribozyme is a fairly rigid entity.
22. Prody G.A., Bakos J.T., Buzayan J.M., Schneider I.R., and Breuning G. Autolytic processing of dimeric plant virus satellite RNA. Science 231 (1986) 1577-1580
23. Pley H.W., Flaherty K.M., and McKay D.B. Three-dimensional structure of a hammerhead ribozyme. Nature 372 (1994) 68-74
24. Scott W.G., Finch J.T., and Klug A. The crystal structure of an all-RNA hammerhead ribozyme. Nucleic Acids Symp Ser 34 (1995) 214-216
25. Martick M., and Scott W.G. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126 (2006) 309-320. A new structure of the hammerhead ribozyme includes a set of distal tertiary contacts neglected by the field between 1987 and 2003. When present, these contacts stabilize the hammerhead active site in a conformation compatible with the known in-line attack mechanism and acid-base catalysis involving two invariant guanosines.
26. Nelson J.A., and Uhlenbeck O.C. When to believe what you see. Mol Cell 23 (2006) 447-450. A review of the more than 12 years of discord in the hammerhead ribozyme field and how many of the apparently irreconcilable differences have been resolved by the new hammerhead structure.
27. Westhof E. A tale in molecular recognition: the hammerhead ribozyme. J Mol Recognit 20 (2006) 1-3. A description of the rediscovery of the importance of tertiary contacts distant from the active site in the hammerhead ribozyme, and a perspective on the relationship between the minimal and full-length hammerhead ribozyme structures.
28. Robertson M.P., and Scott W.G. The structural basis of ribozyme-catalyzed RNA assembly. Science 315 (2007) 1549-1553. L1 ligase is an in vitro evolved and selected ligase that regiospecifically catalyses a 3′ to 5′ phosphodiester bond ligation reaction, a prerequisite for RNA assembly in modern polymerases as well as putative 'RNA world' self-replicating ribozymes. The structure is presented in the form of a ligation product in two conformational states.
29. Joyce G.F. A glimpse of biology's first enzyme. Science 315 (2007) 1507-1508. The L1 ligase structure is placed into the context of possible 'RNA world' evolution scenarios by one of the experts on molecular evolution and the origin of life.