NMR structure of stem-loop D from human rhinovirus-14

RNA

Volumn 13, Issue 3, 2007, Pages 351-360

  Headey, Stephen J ^a   Huang, He ^b,e   Claridge, Jolyon K ^a   Soares, Giselle A ^a   Dutta, Kaushik ^c   Schwalbe, Martin ^a   Yang, Daiwen ^d   Pascal, Steven M ^a  

^a MASSEY UNIVERSITY   (New Zealand)

^b UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^c NEW YORK STRUCTURAL BIOLOGY CENTER   (United States)

^d NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^e VACCINEX INC   (United States)

Author keywords

3Cpro; NMR; Picornavirus; Replication; Rhinovirus; RNA

Indexed keywords

VIRUS RNA;

ARTICLE; HUMAN RHINOVIRUS; HYDROGEN BOND; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PICORNAVIRUS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; RECEPTOR BINDING; SURFACE PROPERTY; VIRUS REPLICATION;

CARBOHYDRATES; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID CONFORMATION; PYRIMIDINES; RHINOVIRUS; RNA, VIRAL;

HUMAN RHINOVIRUS 14; PICORNAVIRIDAE; RHINOVIRUS;

EID: 33847324499     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.313707     Document Type: Article

References (36)

1. Allain, F.H. and Varani, G. 1995. Structure of the P1 helix from group I self-splicing introns. J. Mol. Biol. 250: 333-353.
2. Amineva, S.P., Aminev, A.G., Palmenberg, A.C., and Gern, J.E. 2004. Rhinovirus 3C protease precursors 3CD and 3CD′ localize to the nuclei of infected cells. J. Gen. Virol. 85: 2969-2979.
3. pro) gene of poliovirus can suppress a mutation in the 5′ noncoding region. J. Virol. 64: 607-612.
4. Blair, W.S., Parsley, T.B., Bogerd, H.P., Towner, J.S., Semler, B.L., and Cullen, B.R. 1998. Utilization of a mammalian cell-based RNA binding assay to characterize the RNA binding properties of picornavirus 3C proteases. RNA 4: 215-225.
5. Cheong, H.K., Hwang, E., Lee, C., and Choi, B.S. 2004. Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography. Nucleic Acids Res. 32: e84.
6. Delaglio, F., Greziek, S., Vuister, G.W., Zhu, G., Pfeifer, J., and Bax, A. 1995. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6: 277-293.
7. Du, Z., Yu, J., Andino, R., and James, T.L. 2003. Extending the family of UNCG-like tetraloop motifs: NMR structure of a CACG tetraloop from coxsackievirus B3. Biochemistry 42: 4373-4383.
8. Du, Z., Yu, J., Ulyanov, N.B., Andino, R., and James, T.L. 2004. Solution structure of a consensus stem-loop D RNA domain that plays important roles in regulating translation and replication in enteroviruses and rhinoviruses. Biochemistry 43: 11959-11972.
9. 2-actinomycin D complex. Biochemistry 23: 6717-6723.
10. Greenberg, S.B. 2003. Respiratory consequences of rhinovirus infection. Arch. Intern. Med. 163: 278-284.
11. Hayden, F.G. 2004. Rhinovirus and the lower respiratory tract. Rev. Med. Virol. 14: 17-31.
12. Herold, J. and Andino, R. 2001. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 7: 581-591.
13. Huang, H., Alexandrov, A., Chen, X., Barnes III, T.W., Zhang, H., Dutta, K., and Pascal, S.M. 2001. Structure of an RNA hairpin from HRV-14. Biochemistry 40: 8055-8064.
14. Johnson, B.A. and Blevins, R.A. 1994. NMRView: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4: 603-614.
15. Johnson, V.A. and Semler, B.L. 1988. Defined recombinants of poliovirus and coxsackievirus: Sequence-specific deletions and functional substitutions in the 5′ noncoding regions of viral RNAs. Virology 162: 47-57.
16. Kuyumcu-Martinez, N.M., Van Eden, M.E., Younan, P., and Lloyd, R.E. 2004. Cleavage of poly(A)-binding protein by poliovirus 3C protease inhibits host cell translation: A novel mechanism for host translation shutoff. Mol. Cell. Biol. 24: 1779-1790.
17. Lawrence, C. and Thatch, R. 1975. Identification of a viral protein involved in post-translational maturation of the encephalomyocarditis virus capsid precursor. J. Virol. 15: 918-928.
18. pro has different domains for the RNA binding and proteolytic activities. J. Biol. Chem. 268: 25735-25739.
19. Matthews, D.A., Smith, W.W., Ferre, R.A., Condon, B., Budahazi, G., Sisson, W., Villafranca, J.E., Janson, C.A., McElroy, H.E., and Gribskov, C.L. 1994. Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell 77: 761-771.
20. Mauffret, O., Tevanian, G., and Fermandjian, S. 2002. Residual dipolar coupling constants and structure determination of large DNA duplexes. J. Biomol. NMR 24: 317-328.
21. Meredith, J.M., Rohll, J.B., Almond, J.W., and Evans, D.J. 1999. Similar interactions of the poliovirus and rhinovirus 3D polymerase with the 3′ untranslated region of rhinovirus 14. J. Virol. 73: 9952-9958.
22. Milligan, J.F., Groebe, D.R., Witherell, G.W., and Uhlenbeck, O.C. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15: 8783-8798.
23. Ohlenschlager, O., Wohnert, J., Bucci, E., Seitz, S., Hafner, S., Ramachandran, R., Zell, R., and Gorlach, M. 2004. The structure of the stem-loop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C. Structure 12: 237-248.
24. Pelham, H.R.B. 1978. Translation of encephalomyocarditis virus RNA in vitro yeilds an active proteolytic processing enzyme. Eur. J. Biochem. 85: 457-462.
25. Rieder, E., Xiang, W., Paul, A., and Wimmer, E. 2003. Analysis of the cloverleaf element in a human rhinovirus type 14/poliovirus chimera: Correlation of subdomain D structure, ternary protein complex formation and virus replication. J. Gen. Virol. 84: 2203-2216.
26. Rohll, J.B., Percy, N., Ley, R., Evans, D.J., Almond, J.W., and Barclay, W.S. 1994. The 5′-untranslated regions of picornavirus RNAs contain independent functional domains essential for RNA replication and translation. J. Virol. 68: 4384-4391.
27. Santoro, S.W. and Joyce, G.F. 1997. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. 94: 4262-4266.
28. Sarnow, P. 1989. Role of 3′-end sequence in infectivity of poliovirus transcripts made in vitro. J. Virol. 60: 1040-1049.
29. Todd, S. and Semler, B.L. 1996. Structure-infectivity analysis of the human rhinovirus genomic RNA 3′ non-coding region. Nucleic Acids Res. 24: 2133-2142.
30. Varani, G., Cheong, C., and Tinoco, I. 1991. Structure of an unusually stable RNA hairpin. Biochemistry 30: 3280-3289.
31. Walker, P.A., Leong, L.E., and Porter, A.G. 1995. Sequence and structural determinants of the interaction between the 5′-noncoding region of picornavirus RNA and rhinovirus protease 3C. J. Biol. Chem. 270: 14510-14516.
32. Warren, J.J. and Moore, P.B. 2001. Application of dipolar coupling data to the refinement of the solution structure of the Sarcin-Ricin loop RNA. J. Biomol. NMR 20: 311-323.
33. Wyatt, J.R., Chastain, M., and Puglisi, J.D. 1991. Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques 11: 764-769.
34. pro of poliovirus is essential for RNA replication. J. Virol. 69: 3658-3667.
35. Zell, R., Sidigi, K., Bucci, E., Stelzner, A., and Gorlach, M. 2002. Determinants of the recognition of enteroviral cloverleaf RNA by coxsackievirus B3 proteinase 3C. RNA 8: 188-201.
36. Zweckstetter, M. and Bax, A. 2000. Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR. J. Am. Chem. Soc. 122: 3791-3792.