Crystal structure of a bacterial class 2 histone deacetylase homologue

Journal of Molecular Biology

Volumn 354, Issue 1, 2005, Pages 107-120

  Nielsen, Tine Kragh ^a   Hildmann, Christian ^a   Dickmanns, Achim ^a   Schwienhorst, Andreas ^a   Ficner, Ralf ^a  

^a Inst fuer Mikrobiologie und Genetik   (Germany)

Author keywords

Amidohydrolase; Histone deacetylase; SAHA; X ray crystallography; Zinc ion

Indexed keywords

ACETIC ACID; ACETIC ACID DERIVATIVE; BACTERIAL ENZYME; HISTONE DEACETYLASE 2; HISTONE DEACETYLASE INHIBITOR; HYDROXAMIC ACID DERIVATIVE; VORINOSTAT; ZINC ION;

ACETYLATION; ALCALIGENES; ANTINEOPLASTIC ACTIVITY; ARTICLE; BACTERIAL STRAIN; BORDETELLA; CATALYST; CHEMICAL REACTION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME BINDING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

ALCALIGENES; BACTERIA (MICROORGANISMS); BORDETELLA;

EID: 27344457467     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.09.065     Document Type: Article

References (55)

1. S. Khochbin, and A.P. Wolffe The origin and utility of histone deacetylases FEBS Letters 419 1997 157 160
2. D.D. Leipe, and D. Landsman Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily Nucl. Acids Res. 25 1997 3693 3697
3. I.V. Gregoretti, Y.M. Lee, and H.V. Goodson Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis J. Mol. Biol. 338 2004 17 31
4. M. Grunstein Histone acetylation in chromatin structure and transcription Nature 389 1997 349 352
5. P.A. Wade, D. Pruss, and A.P. Wolffe Histone acetylation: chromatin in action Trends Biochem. Sci. 22 1997 128 132
6. C.L. Peterson HDAC's at work: everyone doing their part Mol. Cell 9 2002 921 922
7. R.J. Lin, L. Nagy, S. Inoue, W. Shao, W.H. Miller Jr, and R.M. Evans Role of the histone deacetylase complex in acute promyelocytic leukaemia Nature 391 1998 811 814
8. F. Grignani, S. De Matteis, C. Nervi, L. Tomassoni, V. Gelmetti, and M. Cioce Fusion proteins of the retinoic acid receptor-alpha recruit histone deacetylase in promyelocytic leukaemia Nature 391 1998 815 818
9. S. Minucci, C. Nervi, F. Lo Coco, and P.G. Pelicci Histone deacetylases: a common molecular target for differentiation treatment of acute myeloid leukemias? Oncogene 20 2001 3110 3115
10. R.W. Johnstone Histone-deacetylase inhibitors: novel drugs for the treatment of cancer Nature Rev. Drug Discov. 1 2002 287 299
11. R.R. Rosato, and S. Grant Histone deacetylase inhibitors in cancer therapy Cancer Biol. Ther. 2 2003 30 37
12. A. Villar-Garea, and M. Esteller Histone deacetylase inhibitors: understanding a new wave of anticancer agents Int. J. Cancer 112 2004 171 178
13. T. Kouzarides Acetylation: a regulatory modification to rival phosphorylation? EMBO J. 19 2000 1176 1179
14. C. Hubbert, A. Guardiola, R. Shao, Y. Kawaguchi, A. Ito, and A. Nixon HDAC6 is a microtubule-associated deacetylase Nature 417 2002 455 458
15. Y. Zhang, N. Li, C. Caron, G. Matthias, D. Hess, S. Khochbin, and P. Matthias HDAC-6 interacts with and deacetylates tubulin and microtubules in vivo EMBO J. 22 2003 1168 1179
16. A. Matsuyama, T. Shimazu, Y. Sumida, A. Saito, Y. Yoshimatsu, and D. Seigneurin-Berny In vivo destabilization of dynamic microtubules by HDAC6-mediated deacetylation EMBO J. 21 2002 6820 6831
17. C. Hildmann, M. Ninkovic, R. Dietrich, D. Wegener, D. Riester, and T. Zimmermann A new amidohydrolase from Bordetella or Alcaligenes strain FB188 with similarities to histone deacetylases J. Bacteriol. 186 2004 2328 2339
18. S. Imai, C.M. Armstrong, M. Kaeberlein, and L. Guarente Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase Nature 403 2000 795 800
19. A.J. de Ruijter, A.H. van Gennip, H.N. Caron, S. Kemp, and A.B. van Kuilenburg Histone deacetylases (HDACs): characterization of the classical HDAC family Biochem. J. 370 2003 737 749
20. C.M. Grozinger, and S.L. Schreiber Deacetylase enzymes: biological functions and the use of small-molecule inhibitors Chem. Biol. 9 2002 3 16
21. N.R. Bertos, A.H. Wang, and X.J. Yang Class II histone deacetylases: structure, function, and regulation Biochem. Cell. Biol. 79 2001 243 252
22. W. Fischle, V. Kiermer, F. Dequiedt, and E. Verdin The emerging role of class II histone deacetylases Biochem. Cell. Biol. 79 2001 337 348
23. D. Seigneurin-Berny, A. Verdel, S. Curtet, C. Lemercier, J. Garin, S. Rousseaux, and S. Khochbin Identification of components of the murine histone deacetylase 6 complex: link between acetylation and ubiquitination signaling pathways Mol. Cell. Biol. 21 2001 8035 8044
24. L. Gao, M.A. Cueto, F. Asselbergs, and P. Atadja Cloning and functional characterization of HDAC11, a novel member of the human histone deacetylase family J. Biol. Chem. 277 2002 25748 25755
25. B. Heltweg, F. Dequiedt, B.L. Marshall, C. Brauch, M. Yoshida, and N. Nishino Subtype selective substrates for histone deacetylases J. Med. Chem. 47 2004 5235 5243
26. A. Mai, S. Massa, R. Pezzi, D. Rotili, P. Loidl, and G. Brosch Discovery of (aryloxopropenyl)pyrrolyl hydroxyamides as selective inhibitors of class IIa histone deacetylase homologue HD1-A J. Med. Chem. 46 2003 4826 4829
27. R. Furumai, Y. Komatsu, N. Nishino, S. Khochbin, M. Yoshida, and S. Horinouchi Potent histone deacetylase inhibitors built from trichostatin A and cyclic tetrapeptide antibiotics including trapoxin Proc. Natl Acad. Sci. USA 98 2001 87 92
28. K.M. Koeller, S.J. Haggarty, B.D. Perkins, I. Leykin, J.C. Wong, M.C. Kao, and S.L. Schreiber Chemical genetic modifier screens: small molecule trichostatin suppressors as probes of intracellular histone and tubulin acetylation Chem. Biol. 10 2003 397 410
29. M.S. Finnin, J.R. Donigian, A. Cohen, V.M. Richon, R.A. Rifkind, and P.A. Marks Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors Nature 401 1999 188 193
30. J.R. Somoza, R.J. Skene, B.A. Katz, C. Mol, J.D. Ho, and A.J. Jennings Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases Structure (Camb.) 12 2004 1325 1334
31. A. Vannini, C. Volpari, G. Filocamo, E.C. Casavola, M. Brunetti, and D. Renzoni Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor Proc. Natl Acad. Sci. USA 101 2004 15064 15069
32. M.M. Harding Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium Acta Crystallog. sect. D 58 2002 872 874
33. D.F. Wang, O. Wiest, P. Helquist, H.Y. Lan-Hargest, and N.L. Wiech On the function of the 14 Å long internal cavity of histone deacetylase-like protein: implications for the design of histone deacetylase inhibitors J. Med. Chem. 47 2004 3409 3417
34. C.S. Craik, S. Roczniak, C. Largman, and W.J. Rutter The catalytic role of the active site aspartic acid in serine proteases Science 237 1987 909 913
35. S. Sprang, T. Standing, R.J. Fletterick, R.M. Stroud, J. Finer-Moore, and N.H. Xuong The three-dimensional structure of Asn102 mutant of trypsin: role of Asp102 in serine protease catalysis Science 237 1987 905 909
36. K. Vanommeslaeghe, C. Van Alsenoy, F. De Proft, J.C. Martins, D. Tourwé, and P. Geelings Ab initio study of the binding of Trichostatin A in the active site of histone deacetylase like protein (HDLP) Org. Biomol. Chem. 1 2003 2951 2957
37. C.M. Grozinger, C.A. Hassig, and S.L. Schreiber Three proteins define a class of human histone deacetylases related to yeast Hda1p Proc. Natl Acad. Sci. USA 96 1999 4868 4873
38. S.J. Haggarty, K.M. Koeller, J.C. Wong, C.M. Grozinger, and S.L. Schreiber Domain-selective small-molecule inhibitor of histone deacetylase 6 (HDAC6)-mediated tubulin deacetylation Proc. Natl Acad. Sci. USA 100 2003 4389 4394
39. H.P. Erickson FtsZ, a prokaryotic homolog of tubulin? Cell 80 1995 367 370
40. R. Ramakrishnan, M. Schuster, and R.B. Bourret Acetylation of Lys-92 enhances signaling by the chemotaxis response regulator protein CheY Proc. Natl Acad. Sci. USA 95 1998 4918 4923
41. K. Reuter, S. Nottrott, P. Fabrizio, R. Lührmann, and R. Ficner Identification, characterization and crystal structure analysis of the human spliceosomal U5 snRNP-specific 15 kDa protein J. Mol. Biol. 294 1999 515 525
42. B.W. Matthews Solvent content of protein crystals J. Mol. Biol. 33 1968 491 497
43. T. Pape, and T.R. Schneider HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs J. Appl. Crystallog. 37 2004 843 844
44. T.C. Terwilliger, and J. Berendzen Automated MAD and MIR structure solution Acta Crystallog. sect. D 55 1999 849 861
45. T.C. Terwilliger Reciprocal-space solvent flattening Acta Crystallog. sect. D 55 1999 1863 1871
46. D.E. McRee XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165
47. T.A. Jones, J.Y. Zou, S.W. Cowan, and Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
48. G.N. Murshudov, A.A. Vagin, A. Lebedev, K.S. Wilson, and E.J. Dodson Efficient anisotropic refinement of macromolecular structures using FFT Acta Crystallog. sect. D 55 1999 247 255
49. A.T. Brunger Assessment of phase accuracy by cross validation: the free R value. Methods and applications Acta Crystallog. sect. D 49 1993 24 36
50. A. Perrakis, R. Morris, and V.S. Lamzin Automated protein model building combined with iterative structure refinement Nature Struct. Biol. 6 1999 458 463
51. A. Vagin, and A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallog. 30 1997 1022 1025
52. A.W. Schuttelkopf, and D.M. van Aalten PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallog. sect. D 60 2004 1355 1363
53. 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. Crystallog. 26 1993 283 291
54. G.J. Kleywegt Use of non-crystallographic symmetry in protein structure refinement Acta Crystallog. sect. D 52 1996 842 857
55. D. Wegener, C. Hildmann, D. Riester, and A. Schwienhorst Improved fluorogenic histone deacetylase assay for high-throughput-screening applications Anal. Biochem. 321 2003 202 208