Recognition of polyadenylate RNA by the poly(A)-binding protein

Cell

Volumn 98, Issue 6, 1999, Pages 835-845

  Deo, Rahul C ^a   Bonanno, Jeffrey B ^a   Sonenberg, Nahum ^b   Burley, Stephen K ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; POLYADENYLATED RNA;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA ANALYSIS; RNA BINDING; RNA CONFORMATION; TRANSLATION INITIATION;

EUKARYOTA;

EID: 0033578927     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81517-2     Document Type: Article

References (47)

1. Adam, S.A., Nakagawa, T., Swanson, M.S., Woodruff, T.K., and Dreyfuss, G. (1986). mRNA polyadenylate-binding protein: gene isolation and sequencing and identification of a ribonucleoprotein consensus sequence. Mol. Cell. Biol. 6, 2932-2943.
2. Afonina, E., Stauber, R., and Pavlakis, G.N. (1998). The human poly(A)-binding protein 1 shuttles between the nucleus and the cytoplasm. J. Biol. Chem. 273, 13015-13021.
3. Baer, B.W., and Kornberg, R.D. (1980). Repeating structure of cytoplasmic poly(A)-ribonucleoprotein. Proc. Natl. Acad. Sci. USA 77, 1890-1892.
4. Baer, B.W., and Kornberg, R.D. (1983). The protein responsible for the repeating structure of cytoplasmic poly(A)-ribonucleoprotein. J. Cell Biol. 96, 717-721.
5. Blobel, G. (1973). A protein of molecular weight 78,000 bound to the polyadenylate region of eukaryotic messenger RNAs. Proc. Natl. Acad. Sci. USA 70, 924-928.
6. Brünger, A.T. (1992a). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
7. Brünger, A.T. (1992b). X-PLOR: a system for X-ray crystallography and NMR (New Haven, CT: Yale University Press).
8. Brünger, A., Adams, P.D., Clore, G.M., Gros, P., Grosse-Kuntsleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., and Read, R.J. (1998). Crystallography and NMR system: a new software system for macromolecular structure determination. Acta Crystallogr. D 54, 905-921.
9. Burd, C.G., and Dreyfuss, G. (1994). Conserved structures and diversity of functions of RNA-binding proteins. Science 265, 615-621.
10. Burd, C.G., Matunis, E.L., and Dreyfuss, G. (1991). The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities. Mol. Cell. Biol. 11, 3419-3424.
11. Carson, M. (1991). RIBBONS 2.0. J. Appl. Crystallogr. 24, 958-961.
12. Craig, A.W., Haghighat, A., Yu, A.T., and Sonenberg, N. (1998). Interaction of polyadenylate-binding protein with the elF4G homologue PAIP enhances translation. Nature 392, 520-523.
13. de La Fortelle, E., and Bricogne, G. (1997). Maximum-likelihood heavy atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-494.
14. Deardorff, J.A., and Sachs, A.B. (1997). Differential effects of aromatic and charged residue substitutions in the RNA binding domains of the yeast poly(A)-binding protein. J. Mol. Biol. 269, 67-81.
15. Ding, J., Hayashi, M.K., Zhang, Y., Manche, L., Krainer, A.R., and Xu, R.M. (1999). Crystal structure of the two-RRM domains of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev. 13, 1102-1115.
16. Gallie, D.R. (1991). The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency. Genes Dev. 5, 2108-2116.
17. Gilson, M., Sharp, K., and Honig, B. (1988). Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comput. Chem. 9, 327-335.
18. Gingras, A.-C., Raught, B., and Sonenberg, N. (1999). elF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu. Rev. Biochem. 68, 913-963.
19. Handa, N., Nureki, O., Kurimoto, K., Kim, I., Sakamoto, H., Shimura, Y., Muto, Y., and Yokoyama, S. (1999). Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 398, 579-585.
20. Imataka, H., Gradi, A., and Sonenberg, N. (1998). A newly identified N-terminal amino acid sequence of human elF4G binds poly(A)-binding protein and functions in poly(A)-dependent translation. EMBO J. 17, 7480-7489.
21. Jacobson, A. (1996) Poly(A) metabolism and translation: the closed loop model. In Translational Control, J.W.B. Hershey, M.B. Mathews, and N. Sonenberg, eds. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory), pp. 451-480.
22. Jessen, T.H., Oubridge, C., Teo, C.H., Pritchard, C., and Nagai, K. (1991). Identification of molecular contacts between the U1A small nuclear ribonucleoprotein and U1 RNA. EMBO J. 10, 3447-3456.
23. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119.
24. Kessler, S.H., and Sachs, A.B. (1998). RNA recognition motif 2 of yeast Pab1 p is required for its functional interaction with eukaryotic translation initiation factor 4G. Mol. Cell. Biol. 18, 51-57.
25. Kuhn, U., and Pieler, T. (1996). Xenopus poly(A) binding protein: functional domains in RNA binding and protein-protein interaction. J. Mol. Biol. 256, 20-30.
26. Laskowski, R.J., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993). PROCHECK: a program to check stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-290.
27. Minvielle-Sebastia, L, Preker, P.J., Wiederkehr, T., Strahm, Y., and Keller, W. (1997). The major yeast poly(A)-binding protein is associated with cleavage factor IA and functions in premessenger RNA 3′-end formation. Proc. Natl. Acad. Sci. USA 94, 7897-7902.
28. Munroe, D., and Jacobson, A. (1990). mRNA poly(A) tail, a 3′ enhancer of translational initiation. Mol. Cell. Biol. 10, 3441-3455.
29. Nagai, K. (1996). RNA-protein complexes. Curr. Opin. Struct. Biol. 6, 53-61.
30. Nicholls, A., Sharp, K., and Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11, 281-296.
31. Nietfeld, W., Mentzel, H., and Pieler, T. (1990). The Xenopus laevis poly(A) binding protein is composed of multiple functionally independent RNA binding domains. EMBO J. 9, 3699-3705.
32. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
33. Oubridge, C., Ito, N., Evans, P.R., Teo, C.H., and Nagai, K. (1994). Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372, 432-438.
34. Piron, M., Vende, P., Cohen, J., and Poncet, D. (1998). Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and evicts the poly(A) binding protein from eIF4F. EMBO J. 17, 5811-5821.
35. Price, S.R., Evans, P.R., and Nagai, K. (1998). Crystal structure of the spliceosomal U2B″-U2A′ protein complex bound to a fragment of U2 small nuclear RNA. Nature 394, 645-650.
36. Sachs, A., and Wahle, E. (1993). Poly(A)tail metabolism and function in eukaryotes. J. Biol. Chem. 268, 22955-22958.
37. Sachs, A.B., Sarnow, P., and Hentze, M.W. (1997). Starting at the beginning, middle, and end - translation initiation in eukaryotes. Cell 89, 831-838.
38. Sali, A., and Blundell, T.L. (1993). Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
39. Scherly, D., Boelens, W., van Venrooij, W.J., Dathan, N.A., Hamm, J., and Mattaj, I.W. (1989). Identification of the RNA binding segment of human U1A protein and definition of its binding site on U1 snRNA. EMBO J. 8, 4163-4170.
40. Shamoo, Y., Abdul-Manan, N., and Williams, K.R. (1995). Multiple RNA binding domains (RBDs) just don't add up. Nucleic Acids Res. 23, 725-728.
41. Shamoo, Y., Krueger, U., Rice, L.M., Williams, K.R., and Steitz, T.A. (1997). Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 Å resolution. Nat. Struct. Biol. 4, 215-222.
42. Sonenberg, N. (1996). mRNA 5′ cap-binding protein eIF4E and control of cell growth. In Translational Control, J.W.B. Hershey, M.B. Mathews, and N. Sonenberg, eds. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory), pp. 245-269.
43. Tarun, S.Z., Jr., and Sachs, A.B. (1995). A common function for mRNA 5′ and 3′ ends in translation initiation in yeast. Genes Dev. 9, 2997-3007.
44. Tarun, S.Z., Wells, S.E., Deardorff, V.A., and Sachs, A. (1997). Translation initiation factor eIF4G mediates in vitro poly (A) tail-dependent translation. Proc. Natl. Acad. Sci. USA 94, 9046-9051.
45. Wahle, E., and Keller, W. (1996). The biochemistry of polyadenylation. Trends Biochem. Sci. 21, 247-250.
46. Wahle, E., Lustig, A., Jeno, P., and Maurer, P. (1993). Mammalian poly(A)-binding protein II. Physical properties and binding to polynucleotides. J. Biol. Chem. 268, 2937-2945.
47. Wells, S.E., Hillner, P.E., Vale, R.D., and Sachs, A.B. (1998). Circularization of mRNA by eukaryotic translation initiation factors. Mol. Cell. 2, 135-140.