Tracing the evolution of the p53 tetramerization domain

Structure

Volumn 22, Issue 9, 2014, Pages 1301-1310

  Joerger, Andreas C ^a   Wilcken, Rainer ^a   Andreeva, Antonina ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN P53; PROTEIN P63; PROTEIN P73; PROTEIN BINDING; ZEBRAFISH PROTEIN;

ALPHA HELIX; ARTICLE; CHEMICAL REACTION; CRYSTAL STRUCTURE; GEL PERMEATION CHROMATOGRAPHY; HUMAN; HYDROGEN BOND; IONIC STRENGTH; NONHUMAN; OLIGOMERIZATION; PH; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TETRAMERIZATION; ZEBRA FISH; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; CONSERVED SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ANALYSIS, PROTEIN; TUMOR SUPPRESSOR PROTEIN P53; ZEBRAFISH; ZEBRAFISH PROTEINS;

EID: 84930190647     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.07.010     Document Type: Article

References (56)

1. P.D. Adams, R.W. Grosse-Kunstleve, L.W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter, and T.C. Terwilliger PHENIX: building new software for automated crystallographic structure determination Acta Crystallogr. D Biol. Crystallogr. 58 2002 1948 1954
2. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
3. V.A. Belyi, P. Ak, E. Markert, H. Wang, W. Hu, A. Puzio-Kuter, and A.J. Levine The origins and evolution of the p53 family of genes Cold Spring Harb. Perspect. Biol. 2 2010 a001198
4. R.R. Betancur, R.E. Broughton, E.O. Wiley, K. Carpenter, J.A. López, C. Li, N.I. Holcroft, D. Arcila, M. Sanciangco, and J.C. Cureton Ii et al. The tree of life and a new classification of bony fishes PLoS Curr. 2013 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 Published online April 18, 2013
5. T. Brandt, M. Petrovich, A.C. Joerger, and D.B. Veprintsev Conservation of DNA-binding specificity and oligomerisation properties within the p53 family BMC Genomics 10 2009 628
6. R.E. Broughton, R. Betancur-R, C. Li, G. Arratia, and G. Ortí Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution PLoS Curr. 2013 10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e Published online April 16, 2013
7. G.M. Clore, J. Ernst, R. Clubb, J.G. Omichinski, W.M. Kennedy, K. Sakaguchi, E. Appella, and A.M. Gronenborn Refined solution structure of the oligomerization domain of the tumour suppressor p53 Nat. Struct. Biol. 2 1995 321 333
8. C. Combet, C. Blanchet, C. Geourjon, and G. Deléage NPS@: network protein sequence analysis Trends Biochem. Sci. 25 2000 147 150
9. D. Coutandin, F. Löhr, F.H. Niesen, T. Ikeya, T.A. Weber, B. Schäfer, E.M. Zielonka, A.N. Bullock, A. Yang, and P. Güntert et al. Conformational stability and activity of p73 require a second helix in the tetramerization domain Cell Death Differ. 16 2009 1582 1589
10. A.D. Cutter Molecular evolution inferences from the C. elegans genome WormBook: the online review of C. elegans biology 2010 1 14
11. C. Dai, and W. Gu p53 post-translational modification: deregulated in tumorigenesis Trends Mol. Med. 16 2010 528 536
12. I.W. Davis, A. Leaver-Fay, V.B. Chen, J.N. Block, G.J. Kapral, X. Wang, L.W. Murray, W.B. Arendall 3rd, J. Snoeyink, J.S. Richardson, and D.C. Richardson MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 2007 W375 W383
13. G.B. Deutsch, E.M. Zielonka, D. Coutandin, T.A. Weber, B. Schäfer, J. Hannewald, L.M. Luh, F.G. Durst, M. Ibrahim, and J. Hoffmann et al. DNA damage in oocytes induces a switch of the quality control factor TAp63α from dimer to tetramer Cell 144 2011 566 576
14. E.L. DiGiammarino, A.S. Lee, C. Cadwell, W. Zhang, B. Bothner, R.C. Ribeiro, G. Zambetti, and R.W. Kriwacki A novel mechanism of tumorigenesis involving pH-dependent destabilization of a mutant p53 tetramer Nat. Struct. Biol. 9 2002 12 16
15. V. Dötsch, F. Bernassola, D. Coutandin, E. Candi, and G. Melino p63 and p73, the ancestors of p53 Cold Spring Harb. Perspect. Biol. 2 2010 a004887
16. A.K. Dunker, I. Silman, V.N. Uversky, and J.L. Sussman Function and structure of inherently disordered proteins Curr. Opin. Struct. Biol. 18 2008 756 764
17. R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
18. P. Emsley, B. Lohkamp, W.G. Scott, and K. Cowtan Features and development of Coot Acta Crystallogr. D Biol. Crystallogr. 66 2010 486 501
19. P. Evans Scaling and assessment of data quality Acta Crystallogr. D Biol. Crystallogr. 62 2006 72 82
20. P.D. Jeffrey, S. Gorina, and N.P. Pavletich Crystal structure of the tetramerization domain of the p53 tumor suppressor at 1.7 angstroms Science 267 1995 1498 1502
21. A.C. Joerger, and A.R. Fersht Structural biology of the tumor suppressor p53 Annu. Rev. Biochem. 77 2008 557 582
22. A.C. Joerger, and A.R. Fersht The tumor suppressor p53: from structures to drug discovery Cold Spring Harb. Perspect. Biol. 2 2010 a000919
23. A.C. Joerger, S. Rajagopalan, E. Natan, D.B. Veprintsev, C.V. Robinson, and A.R. Fersht Structural evolution of p53, p63, and p73: implication for heterotetramer formation Proc. Natl. Acad. Sci. USA 106 2009 17705 17710
24. Z. Johanson, J.A. Long, J.A. Talent, P. Janvier, and J.W. Warren Oldest coelacanth, from the Early Devonian of Australia Biol. Lett. 2 2006 443 446
25. W. Kabsch Xds Acta Crystallogr. D Biol. Crystallogr. 66 2010 125 132
26. N. King, M.J. Westbrook, S.L. Young, A. Kuo, M. Abedin, J. Chapman, S. Fairclough, U. Hellsten, Y. Isogai, and I. Letunic et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans Nature 451 2008 783 788
27. E. Krissinel, and K. Henrick Inference of macromolecular assemblies from crystalline state J. Mol. Biol. 372 2007 774 797
28. D.P. Lane Cancer. p53, guardian of the genome Nature 358 1992 15 16
29. D.P. Lane, C.F. Cheok, C. Brown, A. Madhumalar, F.J. Ghadessy, and C. Verma Mdm2 and p53 are highly conserved from placozoans to man Cell Cycle 9 2010 540 547
30. D.P. Lane, A. Madhumalar, A.P. Lee, B.H. Tay, C. Verma, S. Brenner, and B. Venkatesh Conservation of all three p53 family members and Mdm2 and Mdm4 in the cartilaginous fish Cell Cycle 10 2011 4272 4279
31. G. Langer, S.X. Cohen, V.S. Lamzin, and A. Perrakis Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Nat. Protoc. 3 2008 1171 1179
32. W. Lee, T.S. Harvey, Y. Yin, P. Yau, D. Litchfield, and C.H. Arrowsmith Solution structure of the tetrameric minimum transforming domain of p53 Nat. Struct. Biol. 1 1994 877 890
33. A.J. Levine, R. Tomasini, F.D. McKeon, T.W. Mak, and G. Melino The p53 family: guardians of maternal reproduction Nat. Rev. Mol. Cell Biol. 12 2011 259 265
34. E.D. Levy, E. Boeri Erba, C.V. Robinson, and S.A. Teichmann Assembly reflects evolution of protein complexes Nature 453 2008 1262 1265
35. L.M. Luh, S. Kehrloesser, G.B. Deutsch, J. Gebel, D. Coutandin, B. Schäfer, M. Agostini, G. Melino, and V. Dötsch Analysis of the oligomeric state and transactivation potential of TAp73α Cell Death Differ. 20 2013 1008 1016
36. T.Z. Lwin, J.J. Durant, and D. Bashford A fluid salt-bridging cluster and the stabilization of p53 J. Mol. Biol. 373 2007 1334 1347
37. 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. Cryst. 40 2007 658 674
38. D.W. Meek, and C.W. Anderson Posttranslational modification of p53: cooperative integrators of function Cold Spring Harb. Perspect. Biol. 1 2009 a000950
39. G.N. Murshudov, P. Skubák, A.A. Lebedev, N.S. Pannu, R.A. Steiner, R.A. Nicholls, M.D. Winn, F. Long, and A.A. Vagin REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr. D Biol. Crystallogr. 67 2011 355 367
40. E. Natan, and A.C. Joerger Structure and kinetic stability of the p63 tetramerization domain J. Mol. Biol. 415 2012 503 513
41. T.J. Near, R.I. Eytan, A. Dornburg, K.L. Kuhn, J.A. Moore, M.P. Davis, P.C. Wainwright, M. Friedman, and W.L. Smith Resolution of ray-finned fish phylogeny and timing of diversification Proc. Natl. Acad. Sci. USA 109 2012 13698 13703
42. T.J. Near, A. Dornburg, R.I. Eytan, B.P. Keck, W.L. Smith, K.L. Kuhn, J.A. Moore, S.A. Price, F.T. Burbrink, M. Friedman, and P.C. Wainwright Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes Proc. Natl. Acad. Sci. USA 110 2013 12738 12743
43. A.M. Nedelcu, and C. Tan Early diversification and complex evolutionary history of the p53 tumor suppressor gene family Dev. Genes Evol. 217 2007 801 806
44. J.S. Nelson Fishes of the World Fourth Edition 2006 Wiley New York
45. C.J. Oldfield, J. Meng, J.Y. Yang, M.Q. Yang, V.N. Uversky, and A.K. Dunker Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners BMC Genomics 9 Suppl 1 2008 S1
46. H.D. Ou, F. Löhr, V. Vogel, W. Mäntele, and V. Dötsch Structural evolution of C-terminal domains in the p53 family EMBO J. 26 2007 3463 3473
47. S. Pankow, and C. Bamberger The p53 tumor suppressor-like protein nvp63 mediates selective germ cell death in the sea anemone Nematostella vectensis PLoS ONE 2 2007 e782
48. T. Perica, C. Chothia, and S.A. Teichmann Evolution of oligomeric state through geometric coupling of protein interfaces Proc. Natl. Acad. Sci. USA 109 2012 8127 8132
49. R.A. Pyron Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia Syst. Biol. 60 2011 466 481
50. R. Rutkowski, K. Hofmann, and A. Gartner Phylogeny and function of the invertebrate p53 superfamily Cold Spring Harb. Perspect. Biol. 2 2010 a001131
51. D. San Mauro A multilocus timescale for the origin of extant amphibians Mol. Phylogenet. Evol. 56 2010 554 561
52. V.N. Uversky, V. Davé, L.M. Iakoucheva, P. Malaney, S.J. Metallo, R.R. Pathak, and A.C. Joerger Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases Chem. Rev. 114 2014 6844 6879
53. E. Villiard, H. Brinkmann, O. Moiseeva, F.A. Mallette, G. Ferbeyre, and S. Roy Urodele p53 tolerates amino acid changes found in p53 variants linked to human cancer BMC Evol. Biol. 7 2007 180
54. K.H. Vousden, and C. Prives Blinded by the Light: The Growing Complexity of p53 Cell 137 2009 413 431
55. 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
56. B. Xue, C.J. Brown, A.K. Dunker, and V.N. Uversky Intrinsically disordered regions of p53 family are highly diversified in evolution Biochim. Biophys. Acta 1834 2013 725 738