Solution structure of the ubiquitin-conjugating enzyme UbcH5B

Journal of Molecular Biology

Volumn 344, Issue 2, 2004, Pages 513-526

  Houben, Klaartje ^a   Dominguez, Cyril ^a   Van Schaik, Frederik M A ^b   Timmers, H Th Marc ^b   Bonvin, Alexandre M J J ^a   Boelens, Rolf ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

automated NOE assignment; backbone dynamics; diffusion anisotropy; NMR; ubiquitination

Indexed keywords

ASPARAGINE; UBIQUITIN CONJUGATING ENZYME; UBIQUITIN PROTEIN LIGASE;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; AQUEOUS SOLUTION; ARTICLE; AUTOMATION; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; DATA ANALYSIS; ENZYME ANALYSIS; ENZYME BINDING; ENZYME CONFORMATION; ENZYME STRUCTURE; HYDROGEN BOND; MOLECULAR MODEL; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN FOLDING; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; UBIQUITINATION; X RAY CRYSTALLOGRAPHY;

EUKARYOTA;

EID: 7444234761     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.09.054     Document Type: Article

References (67)

1. A.M. Weissman Themes and variations on ubiquitylation Nature Rev. Mol. Cell. Biol. 2 2001 169 178
2. C.M. Pickart Mechanisms underlying ubiquitination Annu. Rev. Biochem. 70 2001 503 533
3. M.H. Glickman, and A. Ciechanover The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction Physiol. Rev. 82 2002 373 428
4. W. Seufert, and S. Jentsch Ubiquitin-conjugating enzymes UBC4 and UBC5 mediate selective degradation of short-lived and abnormal proteins EMBO J. 9 1990 543 550
5. M. Scheffner, J.M. Huibregtse, and P.M. Howley Identification of a human ubiquitin-conjugating enzyme that mediates the E6-AP-dependent ubiquitination of p53 Proc. Natl Acad. Sci. USA 91 1994 8797 8801
6. H. Gonen, B. Bercovich, A. Orian, A. Carrano, C. Takizawa, and K. Yamanaka Identification of the ubiquitin carrier proteins, E2s, involved in signal-induced conjugation and subsequent degradation of IκBα J. Biol. Chem. 274 1999 14823 14830
7. I. Stancovski, H. Gonen, A. Orian, A.L. Schwartz, and A. Ciechanover Degradation of the proto-oncogene product c-Fos by the ubiquitin proteolytic system in vivo and in vitro: identification and characterization of the conjugating enzymes Mol. Cell. Biol. 15 1995 7106 7116
8. R.C. Aguilar, and B. Wendland Ubiquitin: not just for proteasomes anymore Curr. Opin. Cell. Biol. 15 2003 184 190
9. W.J. Cook, L.C. Jeffrey, M.L. Sullivan, and R.D. Vierstra Three-dimensional structure of a ubiquitin-conjugating enzyme (E2) J. Biol. Chem. 267 1992 15116 15121
10. W.J. Cook, L.C. Jeffrey, Y. Xu, and V. Chau Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4 Biochemistry 32 1993 13809 13817
11. H. Tong, G. Hateboer, A. Perrakis, R. Bernards, and T.K. Sixma Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system J. Biol. Chem. 272 1997 21381 21387
12. W.J. Cook, P.D. Martin, B.F.P. Edwards, R.K. Yamazaki, and V. Chau Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution Biochemistry 36 1997 1621 1627
13. D.K. Worthylake, S. Prakash, L. Prakash, and C.P. Hill Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 Å resolution J. Biol. Chem. 273 1998 6271 6276
14. F. Jiang, and R. Basavappa Crystal structure of the cyclin-specific ubiquitin-conjugating enzyme from clam, E2-C, at 2.0 Å resolution Biochemistry 38 1999 6471 6478
15. K.S. Hamilton, M.J. Ellison, K.R. Barber, R.S. Williams, J.T. Huzil, and S. McKenna Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail Structure 9 2001 897 904
16. A.P. VanDemark, R.M. Hofmann, C. Tsui, C.M. Pickart, and C. Wolberger Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer Cell 105 2001 711 720
17. Y. Lin, W.C. Hwang, and R. Basavappa Structural and functional analysis of the human mitotic-specific ubiquitin-conjugating enzyme, UbcH10 J. Biol. Chem. 277 2002 21913 21921
18. M.F. Giraud, J.M.P. Desterro, and J.H. Naismith Structure of ubiquitin-conjugating enzyme 9 displays significant differences with other ubiquitin-conjugating enzymes which may reflect its specificity for sumo rather than ubiquitin Acta Crystallog. sect. D 54 1998 891 898
19. T. Miura, W. Klaus, A. Ross, P. Güntert, and H. Senn The NMR structure of the class I human ubiquitin-conjugating enzyme 2b J. Biomol. NMR 22 2002 89 92
20. L. Huang, E. Kinnucan, G. Wang, S. Beaudenon, P.M. Howley, J.M. Huibregtse, and N.P. Pavletich Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade Science 286 1999 1321 1326
21. N. Zheng, P. Wang, P.D. Jeffrey, and N.P. Pavletich Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases Cell 102 2000 533 539
22. T.F. Moraes, R.A. Edwards, S. McKenna, L. Pastushok, W. Xiao, J.N. Glover, and M.J. Ellison Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13 Nature Struct. Biol. 8 2001 669 673
23. V. Bernier-Villamor, D.A. Sampson, M.J. Matunis, and C.D. Lima Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1 Cell 108 2002 345 356
24. P.Y. Wu, M. Hanlon, M. Eddins, C. Tsui, R.S. Rogers, and J.P. Jensen A conserved catalytic residue in the ubiquitin-conjugating enzyme family EMBO J. 22 2003 5241 5250
25. N. Tjandra, D.S. Garrett, A.M. Gronenborn, A. Bax, and G.M. Clore Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy Nature Struct. Biol. 4 1997 443 449
26. 15N NMR relaxation J. Am. Chem. Soc. 117 1995 12562 12566
27. R. Brüschweiler, X.B. Liao, and P.E. Wright Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling Science 268 1995 886 889
28. N.A. Farrow, S.J. Archer, Z.J. Wu, D.M. Camac, T. Parsons, M. Rolfe, and P.J. Domaille Backbone resonance assignment of human UBC4 J. Biomol. NMR 18 2000 363 364
29. M. Sattler, J. Schleucher, and C. Griesinger Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients Prog. Nucl. Magn. Reson. Spectrosc. 34 1999 93 158
30. 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
31. J.P. Loria, M. Rance, and A.G. Palmer A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy J. Am. Chem. Soc. 121 1999 2331 2332
32. C. Dominguez, A.M.J.J. Bonvin, G.S. Winkler, F.M.A. van Schaik, H.T.M. Timmers, and R. Boelens Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis and docking approaches Structure 12 2004 633 644
33. 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
34. P. Güntert Automated NMR protein structure calculation Prog. Nucl. Magn. Reson. Spectrosc. 43 2003 105 125
35. 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
36. B.M. Duggan, G.B. Legge, H.J. Dyson, and P.E. Wright SANE (structure assisted NOE evaluation): an automated model-based approach for NOE assignment J. Biomol. NMR 19 2001 321 329
37. B.J. Hare, and G. Wagner Application of automated NOE assignment to three-dimensional structure refinement of a 28 kDa single-chain T cell receptor J. Biomol. NMR 15 1999 103 113
38. P. Güntert, K.D. Berndt, and K. Wüthrich The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein-structure determination J. Biomol. NMR 3 1993 601 606
39. P. Dosset, J.C. Hus, M. Blackledge, and D. Marion Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data J. Biomol. NMR 16 2000 23 28
40. J. Garcia de la Torre, M.L. Huertas, and B. Carrasco HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations J. Magn. Reson. 147 2000 138 146
41. 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR J. Biomol. NMR 23 2002 139 150
42. G. Lipari, and A. Szabo Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of the experimental results J. Am. Chem. Soc. 104 1982 4559 4570
43. Q. Liu, Y.C. Yuan, B.H. Shen, D.J. Chen, and Y. Chen Conformational flexibility of a ubiquitin conjugation enzyme (E2) Biochemistry 38 1999 1415 1425
44. S. Muller, C. Hoege, G. Pyrowolakis, and S. Jentsch SUMO, ubiquitin's mysterious cousin Nature Rev. Mol. Cell. Biol. 2 2001 202 210
45. T.K. Albert, H. Hanzawa, Y.I.A. Legtenberg, M.J. de Ruwe, F.A.J. van den Heuvel, and M.A. Collart Identification of a ubiquitin-protein ligase subunit within the CCR4-NOT transcription repressor complex EMBO J. 21 2002 355 364
46. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
47. M. Nilges, M.J. Macias, S.I. O'Donoghue, and H. Oschkinat Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin J. Mol. Biol. 269 1997 408 422
48. 15N NMR relaxation Biochemistry 33 1994 5984 6003
49. S. Meiboom, and D. Gill Modified spin-echo method for measuring nuclear relaxation times Rev. Sci. Instrum. 29 1958 688 691
50. H.Y. Carr, and E.M. Purcell Effects of diffusion on free precession in nuclear magnetic resonance experiments Phys. Rev. 94 1954 630 638
51. J.W. Peng, V. Thanabal, and G. Wagner 2D heteronuclear NMR measurements of spin-lattice relaxation-times in the rotating frame of X nuclei in heteronuclear HX spin systems J. Magn. Reson. 94 1991 82 100
52. L.E. Kay, L.K. Nicholson, F. Delaglio, A. Bax, and D.A. Torchia Pulse sequences for removal of the effects of cross-correlation between dipolar and chemical-shift anisotropy relaxation mechanism on the measurement of heteronuclear T1 and T2 values in proteins J. Magn. Reson. 97 1992 359 375
53. F.A.A. Mulder, R.A. de Graaf, R. Kaptein, and R. Boelens An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations J. Magn. Reson. 131 1998 351 357
54. D.M. Korzhnev, N.R. Skrynnikov, O. Millet, D.A. Torchia, and L.E. Kay An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates J. Am. Chem. Soc. 124 2002 10743 10753
55. 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
56. 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
57. 13C heteronuclear NMR-spectroscopy J. Am. Chem. Soc. 113 1991 4371 4380
58. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography and NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
59. 15N relaxation parameters J. Biomol. NMR 20 2001 149 165
60. G.M. Clore, A.M. Gronenborn, A. Szabo, and N. Tjandra Determining the magnitude of the fully asymmetric diffusion tensor from heteronuclear relaxation data in the absence of structural information J. Am. Chem. Soc. 120 1998 4889 4890
61. J.P. Linge, M.A. Williams, C.A.E.M. Spronk, A.M.J.J. Bonvin, and M. Nilges Refinement of protein structures in explicit solvent Proteins: Struct. Funct. Genet. 50 2003 496 506
62. R.A. Engh, and R. Huber Accurate bond and angle parameters for X-ray protein-structure refinement Acta Crystallog. sect. A 47 1991 392 400
63. J.P. Linge, M. Habeck, W. Rieping, and M. Nilges Correction of spin diffusion during iterative automated NOE assignment J. Magn. Reson. 167 2004 334 342
64. W.L. Jorgensen, and J. Tirado-Rives The OPLS potential functions for proteins. Energy minimizations for crystals of cyclin peptides and crambin J. Am. Chem. Soc. 110 1988 1657 1666
65. R. Koradi, M. Billeter, and K. Wüthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 51 55 (see also pages 29-32)
66. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystal. 24 1991 946 950
67. E.A. Merritt, and M.E.P. Murphy Raster3D version 2.0: a program for photorealistic molecular graphics Acta Crystallog. sect. D 50 1994 869 873