The C-terminal region of cytoplasmic polyadenylation element binding protein is a ZZ domain with potential for protein-protein interactions

Journal of Molecular Biology

Volumn 425, Issue 11, 2013, Pages 2015-2026

  Merkel, Daniel J ^a   Wells, Sarah B ^a   Hilburn, Bryce C ^a   Elazzouzi, Fatima ^a   Pérez Alvarado, Gabriela C ^a   Lee, Brian M ^a  

^a SOUTHERN ILLINOIS UNIVERSITY   (United States)

Author keywords

RNA binding; SUMO binding domain; translational regulation; zinc binding protein; ZZ motif

Indexed keywords

CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR; CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN; LIM PROTEIN; MESSENGER RNA; POLY(A) RIBONUCLEASE; POLYNUCLEOTIDE ADENYLYLTRANSFERASE; RIBONUCLEASE; RIBONUCLEOPROTEIN; SYMPLEKIN; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; HUMAN; MOLECULAR RECOGNITION; NERVE CELL PLASTICITY; PLANT HOMEODOMAIN; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; PROTEIN SYNTHESIS REGULATION; RING FINGER MOTIF; RNA SEQUENCE; RNA TRANSPORT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SUMOYLATION; ZZ TYPE ZING FINGER DOMAIN;

EID: 84877723134     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.03.009     Document Type: Article

References (69)

1. L. Wu, D. Wells, J. Tay, D. Mendis, M.A. Abbott, and A. Barnitt CPEB-mediated cytoplasmic polyadenylation and the regulation of experience-dependent translation of α-CaMKII mRNA at synapses Neuron 21 1998 1129 1139
2. R. Mendez, and J.D. Richter Translational control by CPEB: a means to the end Nat. Rev., Mol. Cell Biol. 2 2001 521 529
3. H.E. Radford, H.A. Meijer, and C.H. de Moor Translational control by cytoplasmic polyadenylation in Xenopus oocytes Biochim. Biophys. Acta 1779 2008 217 229
4. R. Mendez, L.E. Hake, T. Andresson, L.E. Littlepage, J.V. Ruderman, and J.D. Richter Phosphorylation of CPE binding factor by Eg2 regulates translation of c-mos mRNA Nature 404 2000 302 307
5. H. Kang, and E.M. Schuman A requirement for local protein synthesis in neurotrophin-induced hippocampal synaptic plasticity Science 273 1996 1402 1406
6. K. Si, M. Giustetto, A. Etkin, R. Hsu, A.M. Janisiewicz, and M.C. Miniaci A neuronal isoform of CPEB regulates local protein synthesis and stabilizes synapse-specific long-term facilitation in Aplysia Cell 115 2003 893 904
7. S. Rogers, R. Wells, and M. Rechsteiner Amino acid sequences common to rapidly degraded proteins: the PEST hypothesis Science 234 1986 364 368
8. L.E. Hake, and J.D. Richter CPEB is a specificity factor that mediates cytoplasmic polyadenylation during Xenopus oocyte maturation Cell 79 1994 617 627
9. L.L. McGrew, E. Dworkin-Rastl, M.B. Dworkin, and J.D. Richter Poly(A) elongation during Xenopus oocyte maturation is required for translational recruitment and is mediated by a short sequence element Genes Dev. 3 1989 803 815
10. C.A. Fox, M.D. Sheets, and M.P. Wickens Poly(A) addition during maturation of frog oocytes: distinct nuclear and cytoplasmic activities and regulation by the sequence UUUUUAU Genes Dev. 3 1989 2151 2162
11. L.E. Hake, R. Mendez, and J.D. Richter Specificity of RNA binding by CPEB: requirement for RNA recognition motifs and a novel zinc finger Mol. Cell. Biol. 18 1998 685 693
12. Y.S. Huang, M.C. Kan, C.L. Lin, and J.D. Richter CPEB3 and CPEB4 in neurons: analysis of RNA-binding specificity and translational control of AMPA receptor GluR2 mRNA EMBO J. 25 2006 4865 4876
13. Y. Takagaki, L.C. Ryner, and J.L. Manley Four factors are required for 3′-end cleavage of pre-mRNAs Genes Dev. 3 1989 1711 1724
14. D.C. Barnard, K. Ryan, J.L. Manley, and J.D. Richter Symplekin and xGLD-2 are required for CPEB-mediated cytoplasmic polyadenylation Cell 119 2004 641 651
15. I. Hofmann, M. Schnolzer, I. Kaufmann, and W.W. Franke Symplekin, a constitutive protein of karyo- and cytoplasmic particles involved in mRNA biogenesis in Xenopus laevis oocytes Mol. Biol. Cell 13 2002 1665 1676
16. C.L. Lin, V. Evans, S. Shen, Y. Xing, and J.D. Richter The nuclear experience of CPEB: implications for RNA processing and translational control RNA 16 2009 338 348
17. L. Wang, C.R. Eckmann, L.C. Kadyk, M. Wickens, and J. Kimble A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans Nature 419 2002 312 316
18. J.H. Kim, and J.D. Richter Opposing polymerase-deadenylase activities regulate cytoplasmic polyadenylation Mol. Cell 24 2006 173 183
19. A.L. Lee, R. Kanaar, D.C. Rio, and D.E. Wemmer Resonance assignments and solution structure of the second RNA-binding domain of sex-lethal determined by multidimensional heteronuclear magnetic resonance Biochemistry 33 1994 13775 13786
20. R.C. Deo, J.B. Bonanno, N. Sonenberg, and S.K. Burley Recognition of polyadenylate RNA by the poly(A)-binding protein Cell 98 1999 835 845
21. J.M. Perez-Canadillas Grabbing the message: structural basis of mRNA 3′UTR recognition by Hrp1 EMBO J. 25 2006 3167 3178
22. A.M. Waterhouse, J.B. Procter, D.M. Martin, M. Clamp, and G.J. Barton Jalview version 2 - a multiple sequence alignment editor and analysis workbench Bioinformatics 25 2009 1189 1191
23. G.C. Perez-Alvarado, C. Miles, J.W. Michelsen, H.A. Louis, D.R. Winge, M.C. Beckerle, and M.F. Summers Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP Nat. Struct. Biol. 1 1994 388 398
24. 1H-nuclear magnetic resonance spectroscopy. A new structural class of zinc-finger J. Mol. Biol. 237 1994 201 211
25. 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
26. G.B. Legge, M.A. Martinez-Yamout, D.M. Hambly, T. Trinh, B.M. Lee, H.J. Dyson, and P.E. Wright ZZ domain of CBP: an unusual zinc finger fold in a protein interaction module J. Mol. Biol. 343 2004 1081 1093
27. C.P. Ponting, D.J. Blake, K.E. Davies, J. Kendrick-Jones, and S.J. Winder ZZ and TAZ: new putative zinc fingers in dystrophin and other proteins Trends Biochem. Sci. 21 1996 11 13
28. M.A. Massiah, B.N. Simmons, K.M. Short, and T.C. Cox Solution structure of the RBCC/TRIM B-box1 domain of human MID1: B-box with a RING J. Mol. Biol. 358 2006 532 545
29. J.R. Danielsen, L.K. Povlsen, B.H. Villumsen, W. Streicher, J. Nilsson, and M. Wikstrom DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger J. Cell Biol. 197 2012 179 187
30. V. Vethantham, N. Rao, and J.L. Manley Sumoylation modulates the assembly and activity of the pre-mRNA 3′ processing complex Mol. Cell. Biol. 27 2007 8848 8858
31. T. Herrmann, P. Guntert, and K. Wuthrich 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
32. J.P. Linge, S.I. O'Donoghue, and M. Nilges Automated assignment of ambiguous nuclear overhauser effects with ARIA Methods Enzymol. 339 2001 71 90
33. D.A. Case, T.A. Darden, T.E. Cheatham 3rd, C.L. Simmerling, J. Wang, and R.E. Duke AMBER 10 2008 University of California San Francisco, CA
34. 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
35. R. Koradi, M. Billeter, and K. Wuthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graphics 14 1996 29 32
36. Y.L. Wang, F. Faiola, M. Xu, S. Pan, and E. Martinez Human ATAC is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone fold module that interacts with the TATA-binding protein J. Biol. Chem. 283 2008 33808 33815
37. Y. Nishito, M. Hasegawa, N. Inohara, and G. Nunez MEX is a testis-specific E3 ubiquitin ligase that promotes death receptor-induced apoptosis Biochem. J. 396 2006 411 417
38. 2 zinc-binding domain: insights into an evolutionarily conserved RING fold J. Mol. Biol. 369 2007 1 10
39. N.V. Grishin Treble clef finger - a functionally diverse zinc-binding structural motif Nucleic Acids Res. 29 2001 1703 1714
40. J.H. Laity, B.M. Lee, and P.E. Wright Zinc finger proteins: new insights into structural and functional diversity Curr. Opin. Struct. Biol. 11 2001 39 46
41. J.G. Omichinski, G.M. Clore, O. Schaad, G. Felsenfeld, C. Trainor, and E. Appella NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1 Science 261 1993 438 446
42. 199Hg J couplings in metal-substituted rubredoxin from Pyrococcus furiosus J. Biomol. NMR 2 1992 527 533
43. A. Plechanovova, E.G. Jaffray, S.A. McMahon, K.A. Johnson, I. Navratilova, J.H. Naismith, and R.T. Hay Mechanism of ubiquitylation by dimeric RING ligase RNF4 Nat. Struct. Mol. Biol. 18 2011 1052 1059
44. A. Plechanovova, E.G. Jaffray, M.H. Tatham, J.H. Naismith, and R.T. Hay Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis Nature 489 2012 115 120
45. R. Sanchez, and M.M. Zhou The PHD finger: a versatile epigenome reader Trends Biochem. Sci. 36 2011 364 372
46. R. Budhidarmo, Y. Nakatani, and C.L. Day RINGs hold the key to ubiquitin transfer Trends Biochem. Sci. 37 2012 58 65
47. A.D. Capili, and C.D. Lima Structure and analysis of a complex between SUMO and Ubc9 illustrates features of a conserved E2-Ubl interaction J. Mol. Biol. 369 2007 608 618
48. V. Vethantham, N. Rao, and J.L. Manley Sumoylation regulates multiple aspects of mammalian poly(A) polymerase function Genes Dev. 22 2008 499 511
49. F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, and A. Bax NMRPipe: a multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6 1995 277 293
50. B.A. Johnson, and R.A. Blevins NMRView: a computer program for the visualization and analysis of NMR data J. Biomol. NMR 4 1994 603 614
51. S. Mori, C. Abeygunawardana, M.O. Johnson, and P.C.M. Van Zijl Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation J. Magn. Reson., Ser. B 108 1995 94 98
52. 13C decoupling J. Magn. Reson. 98 1992 428 435
53. A. Bax, R.H. Griffey, and B.L. Hawkins Correlation of proton and nitrogen-15 chemical shifts by multiple quantum NMR J. Magn. Reson. 55 1983 301 315
54. 2O saturation J. Magn. Reson., Ser. A 109 1994 129 133
55. 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
56. S. Grzesiek, and A. Bax Improved 3D triple-resonance NMR techniques applied to a 31 kDa protein J. Magn. Reson. 96 1992 432 440
57. 13C magnetization J. Magn. Reson., Ser. B 101 1993 114 119
58. 13C-labeled proteins via scalar couplings J. Am. Chem. Soc. 115 1993 11054 11055
59. 13C-labeled protein using constant-time evolution J. Biomol. NMR 1 1991 299 304
60. 13C-enriched proteins J. Magn. Reson. 88 1990 425 431
61. K. Wüthrich NMR of proteins and nucleic acids 1986 Wiley New York, NY
62. Y. Shen, F. Delaglio, G. Cornilescu, and A. Bax TALOS plus: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44 2009 213 223
63. J. Jeener, B.H. Meier, P. Bachmann, and R.R. Ernst Investigation of exchange processes by two-dimensional NMR spectroscopy J. Chem. Phys. 71 1979 4546 4553
64. 15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin 1b Biochemistry 28 1989 6150 6156
65. 2O J. Magn. Reson., Ser. B 103 1994 197 201
66. J.G. Pelton, D.A. Torchia, N.D. Meadow, and S. Roseman Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated IIIGlc, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques Protein Sci. 2 1993 543 558
67. P. Guntert, and K. Wuthrich Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints J. Biomol. NMR 1 1991 447 456
68. Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G.M. Xiong, and W. Zhang A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24 2003 1999 2012
69. M.S. Lee, G.P. Gippert, K.V. Soman, D.A. Case, and P.E. Wright Three-dimensional solution structure of a single zinc finger DNA-binding domain Science 245 1989 635 637