Solution structure of the N-terminal zinc fingers of the Xenopus laevis double-stranded RNA-binding protein ZFa

Journal of Molecular Biology

Volumn 351, Issue 4, 2005, Pages 718-730

  Möller, Heiko M ^a,b   Martinez Yamout, Maria A ^a   Dyson, H Jane ^a   Wright, Peter E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

Helix loop helix; Helix turn helix; JAZ; NMR; Wig 1

Indexed keywords

PROTEIN ZFA; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STRUCTURE; RNA BINDING; XENOPUS LAEVIS;

MAMMALIA; XENOPUS LAEVIS;

EID: 23444460429     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.06.032     Document Type: Article

References (55)

1. A.W. Nicholson Structure, reactivity, and biology of double-stranded RNA Prog. Nucl. Acid Res. Mol. Biol. 52 1996 1 65
2. L.R. Saunders, and G.N. Barber The dsRNA binding protein family: critical roles, diverse cellular functions FASEB J. 17 2003 961 983
3. I. Fierro-Monti, and M.B. Mathews Proteins binding to duplexed RNA: one motif, multiple functions Trends Biochem. Sci. 25 2000 241 246
4. E. Bernstein, A.M. Denli, and G.J. Hannon The rest is silence RNA 7 2001 1509 1521
5. W. Saenger Principles of Nucleic Acid Structure 1984 Springer New York
6. C.B. Carlson, O.M. Stephens, and P.A. Beal Recognition of double-stranded RNA by proteins and small molecules Biopolymers 70 2003 86 102
7. R.T. Batey, R.P. Rambo, and J.A. Doudna Tertiary motifs in RNA structure and folding Angew. Chem. (Engl) 38 1999 2327 2343
8. T. Hermann, and D.J. Patel Stitching together RNA tertiary architectures J. Mol. Biol. 294 1999 829 849
9. R. Stefl, L. Skrisovska, and F.H. Allain RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle EMBO Rep. 6 2005 33 38
10. J.M. Ryter, and S.C. Schultz Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA EMBO J. 17 1998 7505 7513
11. A. Ramos, P. Bayer, and G. Varani Determination of the structure of the RNA complex of a double-stranded RNA-binding domain from Drosophila Staufen protein Biopolymers 52 1999 181 196
12. P.J. Finerty, and B.L. Bass A Xenopus zinc finger protein that specifically binds dsRNA and RNA-DNA hybrids J. Mol. Biol. 271 1997 195 208
13. P.J. Finerty, and B.L. Bass Subsets of the zinc finger motifs in dsRBP-ZFa can bind double-stranded RNA Biochemistry 38 1999 4001 4007
14. 2 zinc fingers J. Mol. Biol. 295 2000 719 727
15. S. Varmeh-Ziaie, I. Okan, Y.S. Wang, K.P. Magnusson, P. Warthoe, M. Strauss, and K.G. Wiman Wig-1, a new p53-induced gene encoding a zinc finger protein Oncogene 15 1997 2699 2704
16. D. Israeli, E. Tessler, Y. Haupt, A. Elkeles, S. Wilder, and R. Amson A novel p53-inducible gene, PAG608, encodes a nuclear zinc finger protein whose overexpression promotes apoptosis EMBO J. 16 1997 4384 4392
17. M. Yang, W.S. May, and T. Ito JAZ requires the double-stranded RNA-binding zinc finger motifs for nuclear localization J. Biol. Chem. 274 1999 27399 27406
18. P. Güntert, C. Mumenthaler, and K. Wüthrich Torsion angle dynamics for NMR structure calculation with the new program DYANA J. Mol. Biol. 273 1997 283 298
19. T. Herrmann, P. Güntert, and K. Wüthrich Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA J. Mol. Biol. 319 2002 209 227
20. 15N-enriched proteins J. Am. Chem. Soc. 115 1993 7772 7777
21. G. Cornilescu, F. Delaglio, and A. Bax Protein backbone angle restraints from searching a database for chemical shift and sequence homology J. Biomol. NMR 13 1999 289 302
22. CC couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins J. Biomol. NMR 3 1993 487 493
23. 13C J. Am. Chem. Soc. 115 1993 5334 5335
24. D.A. Case, T. Cheatham, T. Darden, H. Gohlke, R. Luo, and K.M.J. Merz The Amber biomolecular simulation programs J. Comput. Chem. 2005 in the press
25. D. Bashford, and D.A. Case Generalized born models of macromolecular solvation effects Annu. Rev. Phys. Chem. 51 2000 129 152
26. B. Xia, V. Tsui, D.A. Case, H.J. Dyson, and P.E. Wright Comparison of solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model and with explicit water J. Biomol. NMR 22 2002 317 331
27. S. Ludvigsen, and F.M. Poulsen Positive φ-angles in proteins by nuclear magnetic resonance spectroscopy J. Biomol. NMR 2 1992 227 233
28. 13C chemical shifts J. Biomol. NMR 4 1994 455 458
29. J. Pascual, M. Martinez-Yamout, H.J. Dyson, and P.E. Wright Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor J. Mol. Biol. 304 2000 723 729
30. Glc, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques Protein Sci. 2 1993 543 558
31. L. Holm, and C. Sander Dali: a network tool for protein structure comparison Trends Biochem. Sci. 20 1995 478 480
32. E. Krissinel, and K. Henrick Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallog. sect. D 60 2004 2256 2268
33. I. Michalopoulos, G.M. Torrance, D.R. Gilbert, and D.R. Westhead TOPS: an enhanced database of protein structural topology Nucl. Acids Res. 32 2004 D251 D254
34. J.F. Gibrat, T. Madej, and S.H. Bryant Surprising similarities in structure comparison Curr. Opin. Struct. Biol. 6 1996 377 385
35. D.S. Wuttke, M.P. Foster, D.A. Case, J.M. Gottesfeld, and P.E. Wright Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity J. Mol. Biol. 273 1997 183 206
36. R.N. Dutnall, D. Neuhaus, and D. Rhodes The solution structure of the first zinc finger domain of SW15: a novel structural extension to a common fold Structure 4 1996 599 611
37. C.K. Liew, K. Kowalski, A.H. Fox, A. Newton, B.K. Sharpe, M. Crossley, and J.P. Mackay Solution structures of two CCHC zinc fingers from the FOG family protein U-shaped that mediate protein-protein interactions Struct. Fold. Des. 8 2000 1157 1166
38. Y. Muto, D.P. Krummel, C. Oubridge, H. Hernandez, C.V. Robinson, D. Neuhaus, and K. Nagai The structure and biochemical properties of the human spliceosomal protein U1C J. Mol. Biol. 341 2004 185 198
39. H. Aihara, Y. Ito, H. Kurumizaka, T. Terada, S. Yokoyama, and T. Shibata An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing J. Mol. Biol. 274 1997 213 221
40. R.M. Story, I.T. Weber, and T.A. Steitz The structure of the E. coli recA protein monomer and polymer Nature 355 1992 318 325
41. B.L. Bass, S.R. Hurst, and J.D. Singer Binding properties of newly identified Xenopus proteins containing dsRNA-binding motifs Curr. Biol. 4 1994 301 314
42. F. Delaglio, S. Grzesiek, G.W. Vuister, Z. Guang, J. Pfeifer, and A. Bax NMRPipe: a multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6 1995 277 293
43. B.A. Johnson, and R.A. Blevins NMRView: a computer program for the visualization and analysis of NMR data J. Biomol. NMR 4 1994 604 613
44. M. Wittekind, and L. Mueller HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha- and beta-carbon resonances in proteins J. Magn. Reson. 101 1993 201 205
45. S. Grzesiek, and A. Bax Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR J. Am. Chem. Soc. 114 1992 6291 6293
46. 15N-enriched proteins J. Biomol. NMR 3 1993 185 204
47. S.W. Fesik, and E.R.P. Zuiderweg Heteronuclear three-dimensional NMR spectroscopy. A strategy for the simplification of homonuclear two-dimensional NMR spectra J. Magn. Reson. 78 1988 588 593
48. 13C-enriched proteins J. Magn. Reson. 88 1990 425 431
49. 2O solution J. Magn. Reson. 135 1998 185 193
50. S. Grzesiek, H. Kuboniwa, A.P. Hinck, and A. Bax Multiple-quantum line narrowing for measurement of Hα-Hβ J coupling in isotopically enriched proteins J. Am. Chem. Soc. 117 1995 5312 5315
51. 2O in protein NMR. Application to sensitivity enhancement and NOE measurements J. Am. Chem. Soc. 115 1993 12593 12594
52. R.A. Laskowski, J.A.C. Rullmann, M.W. MacArthur, R. Kaptein, and J.M. Thornton AQUA and PROCHECK-NMR programs for checking the quality of protein structures solved by NMR J. Biomol. NMR 8 1996 477 486
53. E.G. Hutchinson, and J.M. Thornton PROMOTIF-A program to identify and analyze structural motifs in proteins Protein Sci. 5 1996 212 220
54. R. Koradi, M. Billeter, and K. Wüthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 51 55
55. C.K. Liew, R.J. Simpson, A.H. Kwan, L.A. Crofts, F.E. Loughlin, and J.M. Matthews Zinc fingers as protein recognition motifs: structural basis for the GATA-1/friend of GATA interaction Proc. Natl Acad. Sci. USA 102 2005 583 588