The Complete VS Ribozyme in Solution Studied by Small-Angle X-Ray Scattering

Structure

Volumn 16, Issue 9, 2008, Pages 1357-1367

  Lipfert, Jan ^a   Ouellet, Jonathan ^b   Norman, David G ^b   Doniach, Sebastian ^a,c   Lilley, David M J ^b  

^a STANFORD UNIVERSITY   (United States)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^c STANFORD UNIVERSITY   (United States)

Author keywords

RNA

Indexed keywords

MAGNESIUM; RIBOZYME; UNCLASSIFIED DRUG; VS RIBOZYME;

ARTICLE; CATALYSIS; ELECTRON; ESTERIFICATION; PRIORITY JOURNAL; PROTEIN FOLDING; RNA SYNTHESIS; X RAY CRYSTALLOGRAPHY;

BASE SEQUENCE; BUFFERS; CATALYTIC DOMAIN; ENDORIBONUCLEASES; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; SCATTERING, SMALL ANGLE; X-RAY DIFFRACTION;

EID: 50649108803     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.07.007     Document Type: Article

References (48)

1. Beattie T.L., Olive J.E., and Collins R.A. A secondary-structure model for the self-cleaving region of Neurospora VS RNA. Proc. Natl. Acad. Sci. USA 92 (1995) 4686-4690
2. Beno M.A., Jennings G., Engbretson M., Knapp G.S., Kurtz C., Zabransky B., Linton J., Seifert S., Wiley C., and Montano P.A. Basic energy sciences synchrotron radiation center undulator sector at the Advanced Photon Source. Nucl. Instrum. Methods Phys. Res. A 467 (2001) 690-693
3. Canny M.D., Jucker F.M., Kellogg E., Khvorova A., Jayasena S.D., and Pardi A. Fast cleavage kinetics of a natural hammerhead ribozyme. J. Am. Chem. Soc. 126 (2004) 10848-10849
4. CCP4 (Collaborative Computational Project, Number 4). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50 (1994) 760-763
5. Cochrane J.C., Lipchock S.V., and Strobel S.A. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem. Biol. 14 (2007) 97-105
6. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, Palo Alto, CA
7. Doniach S. Changes in biomolecular conformations seen by small angle X-ray scattering. Chem. Rev. 101 (2001) 1763-1778
8. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 2126-2132
9. Fedor M.J. Tertiary structure stabilization promotes hairpin ribozyme ligation. Biochemistry 38 (1999) 11040-11050
10. Flinders J., and Dieckmann T. The solution structure of the VS ribozyme active site loop reveals a dynamic "hot-spot.". J. Mol. Biol. 341 (2004) 935-949
11. Guinier A. La diffraction des rayons X aux trés petits angles: application à l'étude de phénomènes ultramicroscopiques. Ann. Phys. 12 (1939) 161-237
12. Guo H.C.T., and Collins R.A. Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA. EMBO J. 14 (1995) 368-376
13. Hampel K.J., and Tinsley M.M. Evidence for preorganization of the glmS ribozyme ligand binding pocket. Biochemistry 45 (2006) 7861-7871
14. Hiley S.L., and Collins R.A. Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme. EMBO J. 20 (2001) 5461-5469
15. Hiley S.L., Sood V.D., Fan J., and Collins R.A. 4-thio-U cross-linking identifies the active site of the VS ribozyme. EMBO J. 21 (2002) 4691-4698
16. Hoffmann B., Mitchell G.T., Gendron P., Major F., Andersen A.A., Collins R.A., and Legault P. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proc. Natl. Acad. Sci. USA 100 (2003) 7003-7008
17. Jones F.D., and Strobel S.A. Ionization of a critical adenosine residue in the Neurospora Varkud satellite ribozyme active site. Biochemistry 42 (2003) 4265-4276
18. Jones F.D., Ryder S.P., and Strobel S.A. An efficient ligation reaction promoted by a Varkud satellite ribozyme with extended 5′- and 3′-termini. Nucleic Acids Res. 29 (2001) 5115-5120
19. Khvorova A., Lescoute A., Westhof E., and Jayasena S.D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat. Struct. Biol. 10 (2003) 708-712
20. Klein D.J., and Ferré-D'Amaré A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313 (2006) 1752-1756
21. Kozin M.B., and Svergun D.I. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 34 (2001) 33-41
22. Lafontaine D.A., Norman D.G., and Lilley D.M.J. Structure, folding, and activity of the VS ribozyme: importance of the 2-3-6 helical junction. EMBO J. 20 (2001) 1415-1424
23. Lafontaine D.A., Wilson T.J., Norman D.G., and Lilley D.M.J. The A730 loop is an important component of the active site of the VS ribozyme. J. Mol. Biol. 312 (2001) 663-674
24. Lafontaine D.A., Norman D.G., and Lilley D.M.J. The global structure of the VS ribozyme. EMBO J. 21 (2002) 2461-2471
25. Lescoute A., and Westhof E. Topology of three-way junctions in folded RNAs. RNA 12 (2006) 83-93
26. In: Lilley D.M.J., and Eckstein F. (Eds). Ribozymes and RNA Catalysis (2008), Royal Society of Chemistry, Cambridge, UK
27. Lipfert J., and Doniach S. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu. Rev. Biophys. Biomol. Struct. 36 (2007) 307-327
28. Lipfert J., Millett I.S., Seifert S., and Doniach S. Sample holder for small-angle X-ray scattering static and flow cell measurements. Rev. Sci. Instrum. 77 (2006) 461081-461084
29. Lipfert J., Chu V.B., Bai Y., Herschlag D., and Doniach S. Low resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling. J. Appl. Crystallogr. 40 (2007) S229-S235
30. Lipfert J., Das R., Chu V.B., Kudaravalli M., Boyd N., Herschlag D., and Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J. Mol. Biol. 365 (2007) 1393-1406
31. McLeod A.C., and Lilley D.M.J. Efficient, pH-dependent RNA ligation by the VS ribozyme in trans. Biochemistry 43 (2004) 1118-1125
32. Murchie A.I.H., Thomson J.B., Walter F., and Lilley D.M.J. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol. Cell 1 (1998) 873-881
33. Penedo J.C., Wilson T.J., Jayasena S.D., Khvorova A., and Lilley D.M.J. Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA 10 (2004) 880-888
34. Rastogi T., Beattie T.L., Olive J.E., and Collins R.A. A long-range pseudoknot is required for activity of the Neurospora VS ribozyme. EMBO J. 15 (1996) 2820-2825
35. Saville B.J., and Collins R.A. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell 61 (1990) 685-696
36. Schwieters C.D., Kuszewski J.J., Tjandra N., and Clore G.M. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160 (2003) 65-73
37. Seifert S., Winans R.E., Tiede D.M., and Thiyagarajan P. Design and performance of a ASAXS instrument at the Advanced Photon Source. J. Appl. Crystallogr. 33 (2000) 782-784
38. Sood V.D., and Collins R.A. Functional equivalence of the uridine turn and the hairpin as building blocks of tertiary structure in the Neurospora VS ribozyme. J. Mol. Biol. 313 (2001) 1013-1019
39. Sood V.D., and Collins R.A. Identification of the catalytic subdomain of the VS ribozyme and evidence for remarkable sequence tolerance in the active site loop. J. Mol. Biol. 320 (2002) 443-454
40. Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25 (1992) 495-503
41. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76 (1999) 2879-2886
42. Svergun D.I., and Koch M.H.J. Small-angle scattering studies of biological macromolecules in solution. Rep. Prog. Phys. 66 (2003) 1735-1782
43. Svergun D.I., Barberato C., and Koch M.H.J. CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28 (1995) 768-773
44. Tan E., Wilson T.J., Nahas M.K., Clegg R.M., Lilley D.M.J., and Ha T. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 9308-9313
45. Volkov V.V., and Svergun D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 36 (2003) 860-864
46. Walter N.G., Burke J.M., and Millar D.P. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nat. Struct. Biol. 6 (1999) 544-549
47. Wilson T.J., McLeod A.C., and Lilley D.M.J. A guanine nucleobase important for catalysis by the VS ribozyme. EMBO J. 26 (2007) 2489-2500
48. Zhao Z.Y., McLeod A., Harusawa S., Araki L., Yamaguchi M., Kurihara T., and Lilley D.M.J. Nucleobase participation in ribozyme catalysis. J. Am. Chem. Soc. 127 (2005) 5026-5027