Crystal structure of the N-terminal domain of Nup358/RanBP2

Journal of Molecular Biology

Volumn 423, Issue 5, 2012, Pages 752-765

  Kassube, Susanne A ^a,c   Stuwe, Tobias ^b   Lin, Daniel H ^b   Antonuk, C Danielle ^b   Napetschnig, Johanna ^a,d   Blobel, Günter ^a   Hoelz, André ^a,b  

^a ROCKEFELLER UNIVERSITY   (United States)

^b California Institute of Technology   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

fluorescence localization microscopy; nuclear pore complex (NPC); RNA binding protein; tetratricopeptide repeat (TPR); X ray crystallography

Indexed keywords

BINDING PROTEIN; NUCLEOPORIN; NUP358 PROTEIN; RAN BINDING PROTEIN 2; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; HUMAN; HYDROPHOBICITY; NONHUMAN; NUCLEAR PORE COMPLEX; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; STATIC ELECTRICITY; STRUCTURE ANALYSIS; SURFACE PROPERTY; TETRATRICOPEPTIDE REPEAT;

EUKARYOTA;

EID: 84867576555     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2012.08.026     Document Type: Article

References (57)

1. A. Hoelz, E.W. Debler, and G. Blobel The structure of the nuclear pore complex Annu. Rev. Biochem. 80 2011 613 643
2. E.W. Debler, K.C. Hsia, V. Nagy, H.S. Seo, and A. Hoelz Characterization of the membrane-coating Nup84 complex: paradigm for the nuclear pore complex structure Nucleus 1 2010 150 157
3. E.W. Debler, Y. Ma, H.S. Seo, K.C. Hsia, T.R. Noriega, G. Blobel, and A. Hoelz A fence-like coat for the nuclear pore membrane Mol. Cell 32 2008 815 826
4. K.C. Hsia, P. Stavropoulos, G. Blobel, and A. Hoelz Architecture of a coat for the nuclear pore membrane Cell 131 2007 1313 1326 (Pubitemid 350297420)
5. S.G. Brohawn, N.C. Leksa, E.D. Spear, K.R. Rajashankar, and T.U. Schwartz Structural evidence for common ancestry of the nuclear pore complex and vesicle coats Science 322 2008 1369 1373 (Pubitemid 352775247)
6. S. Fath, J.D. Mancias, X. Bi, and J. Goldberg Structure and organization of coat proteins in the COPII cage Cell 129 2007 1325 1336 (Pubitemid 46962091)
7. C. Lee, and J. Goldberg Structure of coatomer cage proteins and the relationship among COPI, COPII, and clathrin vesicle coats Cell 142 2010 123 132
8. M. Stewart Ratcheting mRNA out of the nucleus Mol. Cell 25 2007 327 330 (Pubitemid 46199291)
9. J. Wu, M.J. Matunis, D. Kraemer, G. Blobel, and E. Coutavas Nup358, a cytoplasmically exposed nucleoporin with peptide repeats, Ran-GTP binding sites, zinc fingers, a cyclophilin A homologous domain, and a leucine-rich region J. Biol. Chem. 270 1995 14209 14213
10. N. Yokoyama, N. Hayashi, T. Seki, N. Pante, T. Ohba, and K. Nishii A giant nucleopore protein that binds Ran/TC4 Nature 376 1995 184 188
11. A. Cook, F. Bono, M. Jinek, and E. Conti Structural biology of nucleocytoplasmic transport Annu. Rev. Biochem. 76 2007 647 671
12. P.E. Gleizes, J. Noaillac-Depeyre, I. Leger-Silvestre, F. Teulieres, J.Y. Dauxois, and D. Pommet Ultrastructural localization of rRNA shows defective nuclear export of preribosomes in mutants of the Nup82p complex J. Cell Biol. 155 2001 923 936 (Pubitemid 34286244)
13. M.A. Powers, D.J. Forbes, J.E. Dahlberg, and E. Lund The vertebrate GLFG nucleoporin, Nup98, is an essential component of multiple RNA export pathways J. Cell Biol. 136 1997 241 250 (Pubitemid 27063078)
14. T. Stuwe, L. Schada von Borzyskowski, A.M. Davenport, and A. Hoelz Molecular basis for the anchoring of proto-oncoprotein nup98 to the cytoplasmic face of the nuclear pore complex J. Mol. Biol. 419 2012 330 346
15. K. Yoshida, H.S. Seo, E.W. Debler, G. Blobel, and A. Hoelz Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex Proc. Natl Acad. Sci. USA 108 2011 16571 16576
16. C. Schmitt, C. von Kobbe, A. Bachi, N. Pante, J.P. Rodrigues, and C. Boscheron Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p EMBO J. 18 1999 4332 4347 (Pubitemid 29364135)
17. J. Napetschnig, S.A. Kassube, E.W. Debler, R.W. Wong, G. Blobel, and A. Hoelz Structural and functional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19 Proc. Natl Acad. Sci. USA 106 2009 3089 3094
18. H. von Moeller, C. Basquin, and E. Conti The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner Nat. Struct. Mol. Biol. 16 2009 247 254
19. D. Forler, G. Rabut, F.D. Ciccarelli, A. Herold, T. Kocher, and R. Niggeweg RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export Mol. Cell. Biol. 24 2004 1155 1167 (Pubitemid 38112178)
20. M.J. Matunis, J. Wu, and G. Blobel SUMO-1 modification and its role in targeting the Ran GTPase-activating protein, RanGAP1, to the nuclear pore complex J. Cell Biol. 140 1998 499 509 (Pubitemid 28134055)
21. R. Bernad, H. van der Velde, M. Fornerod, and H. Pickersgill Nup358/RanBP2 attaches to the nuclear pore complex via association with Nup88 and Nup214/CAN and plays a supporting role in CRM1-mediated nuclear protein export Mol. Cell. Biol. 24 2004 2373 2384 (Pubitemid 38325994)
22. J. Joseph, and M. Dasso The nucleoporin Nup358 associates with and regulates interphase microtubules FEBS Lett. 582 2008 190 196
23. D. Salina, P. Enarson, J.B. Rattner, and B. Burke Nup358 integrates nuclear envelope breakdown with kinetochore assembly J. Cell Biol. 162 2003 991 1001 (Pubitemid 37174183)
24. C. Slape, and P.D. Aplan The role of NUP98 gene fusions in hematologic malignancy Leuk. Lymphoma 45 2004 1341 1350 (Pubitemid 38701908)
25. A. Kohler, and E. Hurt Gene regulation by nucleoporins and links to cancer Mol. Cell 38 2010 6 15
26. D. Agudo, F. Gomez-Esquer, F. Martinez-Arribas, M.J. Nunez-Villar, M. Pollan, and J. Schneider Nup88 mRNA overexpression is associated with high aggressiveness of breast cancer Int. J. Cancer 109 2004 717 720 (Pubitemid 38405619)
27. R.S. Felix, G.W. Colleoni, O.L. Caballero, M. Yamamoto, M.S. Almeida, and V.C. Andrade SAGE analysis highlights the importance of p53csv, ddx5, mapkapk2 and ranbp2 to multiple myeloma tumorigenesis Cancer Lett. 278 2009 41 48
28. M. von Lindern, M. Fornerod, S. van Baal, M. Jaegle, T. de Wit, A. Buijs, and G. Grosveld The translocation (6;9), associated with a specific subtype of acute myeloid leukemia, results in the fusion of two genes, dek and can, and the expression of a chimeric, leukemia-specific dek-can mRNA Mol. Cell. Biol. 12 1992 1687 1697
29. Z. Ma, D.A. Hill, M.H. Collins, S.W. Morris, J. Sumegi, and M. Zhou Fusion of ALK to the Ran-binding protein 2 (RANBP2) gene in inflammatory myofibroblastic tumor Genes Chromosomes Cancer 37 2003 98 105 (Pubitemid 36417927)
30. D.E. Neilson, M.D. Adams, C.M. Orr, D.K. Schelling, R.M. Eiben, and D.S. Kerr Infection-triggered familial or recurrent cases of acute necrotizing encephalopathy caused by mutations in a component of the nuclear pore, RANBP2 Am. J. Hum. Genet. 84 2009 44 51
31. Y.M. Chook, and G. Blobel Karyopherins and nuclear import Curr. Opin. Struct. Biol. 11 2001 703 715 (Pubitemid 34076632)
32. G.L. Blatch, and M. Lassle The tetratricopeptide repeat: a structural motif mediating protein-protein interactions BioEssays 21 1999 932 939 (Pubitemid 29530602)
33. L.D. D'Andrea, and L. Regan TPR proteins: the versatile helix Trends Biochem. Sci. 28 2003 655 662 (Pubitemid 37500900)
34. E.R. Main, Y. Xiong, M.J. Cocco, L. D'Andrea, and L. Regan Design of stable alpha-helical arrays from an idealized TPR motif Structure 11 2003 497 508 (Pubitemid 36579128)
35. A.K. Das, P.W. Cohen, and D. Barford The structure of the tetratricopeptide repeats of protein phosphatase 5: implications for TPR-mediated protein-protein interactions EMBO J. 17 1998 1192 1199 (Pubitemid 28105498)
36. C. Scheufler, A. Brinker, G. Bourenkov, S. Pegoraro, L. Moroder, and H. Bartunik Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine Cell 101 2000 199 210 (Pubitemid 32004747)
37. M. Jinek, J. Rehwinkel, B.D. Lazarus, E. Izaurralde, J.A. Hanover, and E. Conti The superhelical TPR-repeat domain of O-linked GlcNAc transferase exhibits structural similarities to importin alpha Nat. Struct. Mol. Biol. 11 2004 1001 1007 (Pubitemid 39315305)
38. Y. Ren, H.S. Seo, G. Blobel, and A. Hoelz Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1 Proc. Natl Acad. Sci. USA 107 2010 10406 10411
39. L.I. Davis, and G. Blobel Identification and characterization of a nuclear pore complex protein Cell 45 1986 699 709 (Pubitemid 16063133)
40. B. Montpetit, N.D. Thomsen, K.J. Helmke, M.A. Seeliger, J.M. Berger, and K. Weis A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export Nature 472 2011 238 242
41. S. Doublie Preparation of selenomethionyl proteins for phase determination Methods Enzymol. 276 1997 523 530 (Pubitemid 27085620)
42. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326 (Pubitemid 27085611)
43. G. Bricogne, C. Vonrhein, C. Flensburg, M. Schiltz, and W. Paciorek Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0 Acta Crystallogr., Sect. D: Biol. Crystallogr. 59 2003 2023 2030 (Pubitemid 37399336)
44. Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 1994 760 763
45. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr., Sect. A: Found. Crystallogr. 47 1991 110 119
46. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 2004 2126 2132 (Pubitemid 41742764)
47. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 1998 905 921
48. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, and N. Echols PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr., Sect. D: Biol. Crystallogr. 66 2010 213 221
49. A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J. Appl. Crystallogr. 40 2007 658 674 (Pubitemid 47080256)
50. S. Parsons Introduction to twinning Acta Crystallogr., Sect. D: Biol. Crystallogr. 59 2003 1995 2003 (Pubitemid 37399333)
51. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
52. I.W. Davis, A. Leaver-Fay, V.B. Chen, J.N. Block, G.J. Kapral, and X. Wang MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 2007 W375 W383
53. P.J. Wyatt Multiangle light scattering: the basic tool for macromolecular characterization Instrum. Sci. Technol. 25 1997 1 18 (Pubitemid 127623159)
54. F. Jeanmougin, J.D. Thompson, M. Gouy, D.G. Higgins, and T.J. Gibson Multiple sequence alignment with Clustal X Trends Biochem. Sci. 23 1998 403 405 (Pubitemid 28511382)
55. G.J. Barton ALSCRIPT: a tool to format multiple sequence alignments Protein Eng. 6 1993 37 40 (Pubitemid 23048938)
56. N.A. Baker, D. Sept, S. Joseph, M.J. Holst, and J.A. McCammon Electrostatics of nanosystems: application to microtubules and the ribosome Proc. Natl Acad. Sci. USA 98 2001 10037 10041 (Pubitemid 32802969)
57. R. Koradi, M. Billeter, and K. Wuthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graphics 14 1996 29 32 51-55