Structural and functional analysis of human SIRT1

Journal of Molecular Biology

Volumn 426, Issue 3, 2014, Pages 526-541

  Davenport, Andrew M ^a   Huber, Ferdinand M ^a   Hoelz, André ^a  

^a California Institute of Technology   (United States)

Author keywords

conformational plasticity; enzyme peptide substrate interaction; enzyme regulation; mutational analysis; X ray crystallography

Indexed keywords

HETERODIMER; SIRTUIN 1; NICOTINAMIDE ADENINE DINUCLEOTIDE;

ARTICLE; BETA SHEET; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME STABILITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; GEL PERMEATION CHROMATOGRAPHY; HUMAN; LIGHT SCATTERING; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; X RAY DIFFRACTION; AMINO TERMINAL SEQUENCE; CHEMICAL ANALYSIS; DEACETYLATION; HYDROPHOBICITY; IN VITRO STUDY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; THERMOSTABILITY;

ADENOSINE DIPHOSPHORIBOSE; ADPR; CONFORMATIONAL PLASTICITY; ENZYME PEPTIDE SUBSTRATE INTERACTION; ENZYME REGULATION; GLUTATHIONE S-TRANSFERASE; GST; MALS; MULTIANGLE LIGHT SCATTERING; MUTATIONAL ANALYSIS; SEC; SILENT INFORMATION REGULATOR 2; SIR2; SIZE-EXCLUSION CHROMATOGRAPHY; SSRL; STANFORD SYNCHROTRON RADIATION LIGHTSOURCE; X-RAY CRYSTALLOGRAPHY;

ACETYLATION; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HUMANS; MODELS, MOLECULAR; NAD; PROTEIN CONFORMATION; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SIRTUIN 1;

EID: 84892495970     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.10.009     Document Type: Article

References (66)

1. A.J. Klar, S. Fogel, and K. Macleod MAR1 - a regulator of the HMa and HMα loci in SACCHAROMYCES CEREVISIAE Genetics 93 1979 37 50
2. J.E. Haber, and J.P. George A mutation that permits the expression of normally silent copies of mating-type information in Saccharomyces cerevisiae Genetics 93 1979 13 35
3. J. Rine, J.N. Strathern, J.B. Hicks, and I. Herskowitz A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: evidence for and identification of cryptic mating-type loci Genetics 93 1979 877 901
4. O.M. Aparicio, B.L. Billington, and D.E. Gottschling Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae Cell 66 1991 1279 1287
5. M. Bryk, M. Banerjee, M. Murphy, K.E. Knudsen, D.J. Garfinkel, and M.J. Curcio Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast Genes Dev 11 1997 255 269
6. C.E. Fritze, K. Verschueren, R. Strich, and R. Easton Esposito Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA EMBO J 16 1997 6495 6509
7. J.S. Smith, and J.D. Boeke An unusual form of transcriptional silencing in yeast ribosomal DNA Genes Dev 11 1997 241 254
8. 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
9. J. Landry, A. Sutton, S.T. Tafrov, R.C. Heller, J. Stebbins, and L. Pillus et al. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases Proc Natl Acad Sci USA 97 2000 5807 5811
10. +-dependent protein deacetylase activity in the Sir2 protein family Proc Natl Acad Sci USA 97 2000 6658 6663
11. J.A. Garcia-Salcedo, P. Gijon, D.P. Nolan, P. Tebabi, and E. Pays A chromosomal SIR2 homologue with both histone NAD-dependent ADP- ribosyltransferase and deacetylase activities is involved in DNA repair in Trypanosoma brucei EMBO J 22 2003 5851 5862
12. G. Liszt, E. Ford, M. Kurtev, and L. Guarente Mouse Sir2 homolog SIRT6 is a nuclear ADP-ribosyltransferase J Biol Chem 280 2005 21313 21320
13. A.W. Tsang, and J.C. Escalante-Semerena CobB, a new member of the SIR2 family of eucaryotic regulatory proteins, is required to compensate for the lack of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase activity in cobT mutants during cobalamin biosynthesis in Salmonella typhimurium LT2 J Biol Chem 273 1998 31788 31794
14. T.M. Kowieski, S. Lee, and J.M. Denu Acetylation-dependent ADP-ribosylation by Trypanosoma brucei Sir2 J Biol Chem 283 2008 5317 5326
15. C.J. Merrick, and M.T. Duraisingh Plasmodium falciparum Sir2: an unusual sirtuin with dual histone deacetylase and ADP-ribosyltransferase activity Eukaryot Cell 6 2007 2081 2091
16. M.C. Haigis, R. Mostoslavsky, K.M. Haigis, K. Fahie, D.C. Christodoulou, and A.J. Murphy et al. SIRT4 inhibits glutamate dehydrogenase and opposes the effects of calorie restriction in pancreatic beta cells Cell 126 2006 941 954
17. J. Du, Y. Zhou, X. Su, J.J. Yu, S. Khan, and H. Jiang et al. Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase Science 334 2011 806 809
18. A.A. Sauve, C. Wolberger, V.L. Schramm, and J.D. Boeke The biochemistry of sirtuins Annu Rev Biochem 75 2006 435 465
19. +-dependent deacetylation reactions Biochemistry 40 2001 15456 15463
20. J.L. Avalos, K.M. Bever, and C. Wolberger Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme Mol Cell 17 2005 855 868
21. J.L. Avalos, J.D. Boeke, and C. Wolberger Structural basis for the mechanism and regulation of Sir2 enzymes Mol Cell 13 2004 639 648
22. J.L. Avalos, I. Celic, S. Muhammad, M.S. Cosgrove, J.D. Boeke, and C. Wolberger Structure of a Sir2 enzyme bound to an acetylated p53 peptide Mol Cell 10 2002 523 535
23. M.S. Finnin, J.R. Donigian, and N.P. Pavletich Structure of the histone deacetylase SIRT2 Nat Struct Biol 8 2001 621 625
24. L. Jin, W. Wei, Y. Jiang, H. Peng, J. Cai, and C. Mao et al. Crystal structures of human SIRT3 displaying substrate-induced conformational changes J Biol Chem 284 2009 24394 24405
25. J. Min, J. Landry, R. Sternglanz, and R.M. Xu Crystal structure of a SIR2 homolog-NAD complex Cell 105 2001 269 279
26. K. Zhao, X. Chai, A. Clements, and R. Marmorstein Structure and autoregulation of the yeast Hst2 homolog of Sir2 Nat Struct Biol 10 2003 864 871
27. K. Zhao, X. Chai, and R. Marmorstein Structure of the yeast Hst2 protein deacetylase in ternary complex with 2′-O-acetyl ADP ribose and histone peptide Structure 11 2003 1403 1411
28. K. Zhao, R. Harshaw, X. Chai, and R. Marmorstein Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases Proc Natl Acad Sci USA 101 2004 8563 8568
29. + and acetylated peptide Structure 14 2006 1231 1240
30. J.H. Chang, H.C. Kim, K.Y. Hwang, J.W. Lee, S.P. Jackson, and S.D. Bell et al. Structural basis for the NAD-dependent deacetylase mechanism of Sir2 J Biol Chem 277 2002 34489 34498
31. B.G. Szczepankiewicz, H. Dai, K.J. Koppetsch, D. Qian, F. Jiang, and C. Mao et al. Synthesis of carba-NAD and the structures of its ternary complexes with SIRT3 and SIRT5 J Org Chem 77 2012 7319 7329
32. Y. Zhou, H. Zhang, B. He, J. Du, H. Lin, and R.A. Cerione et al. The bicyclic intermediate structure provides insights into the desuccinylation mechanism of human sirtuin 5 (SIRT5) J Biol Chem 287 2012 28307 28314
33. +- dependent deacetylase SIRT5 by suramin Structure 15 2007 377 389
34. M.S. Cosgrove, K. Bever, J.L. Avalos, S. Muhammad, X. Zhang, and C. Wolberger The structural basis of sirtuin substrate affinity Biochemistry 45 2006 7511 7521
35. A.Y. Zhu, Y. Zhou, S. Khan, K.W. Deitsch, Q. Hao, and H. Lin Plasmodium falciparum Sir2A preferentially hydrolyzes medium and long chain fatty acyl lysine ACS Chem Biol 7 2012 155 159
36. P. Bheda, J.T. Wang, J.C. Escalante-Semerena, and C. Wolberger Structure of Sir2Tm bound to a propionylated peptide Protein Sci 20 2011 131 139
37. W.F. Hawse, K.G. Hoff, D.G. Fatkins, A. Daines, O.V. Zubkova, and V.L. Schramm et al. Structural insights into intermediate steps in the Sir2 deacetylation reaction Structure 16 2008 1368 1377
38. B.D. Sanders, K. Zhao, J.T. Slama, and R. Marmorstein Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes Mol Cell 25 2007 463 472
39. +) and an indole (EX527 analogue) reveals a novel mechanism of histone deacetylase inhibition J Med Chem 56 2013 963 969
40. H.C. Hsu, C.L. Wang, M. Wang, N. Yang, Z. Chen, and R. Sternglanz et al. Structural basis for allosteric stimulation of Sir2 activity by Sir4 binding Genes Dev 27 2013 64 73
41. M.C. Haigis, and D.A. Sinclair Mammalian sirtuins: biological insights and disease relevance Annu Rev Pathol 5 2010 253 295
42. L. Guarente Sirtuins in aging and disease Cold Spring Harbor Symp Quant Biol 72 2007 483 488
43. A.A. Sauve, and V.L. Schramm Sir2 regulation by nicotinamide results from switching between base exchange and deacetylation chemistry Biochemistry 42 2003 9249 9256
44. E.J. Kim, J.H. Kho, M.R. Kang, and S.J. Um Active regulator of SIRT1 cooperates with SIRT1 and facilitates suppression of p53 activity Mol Cell 28 2007 277 290
45. J.E. Kim, J. Chen, and Z. Lou DBC1 is a negative regulator of SIRT1 Nature 451 2008 583 586
46. W. Zhao, J.P. Kruse, Y. Tang, S.Y. Jung, J. Qin, and W. Gu Negative regulation of the deacetylase SIRT1 by DBC1 Nature 451 2008 587 590
47. H. Kang, J.Y. Suh, Y.S. Jung, J.W. Jung, M.K. Kim, and J.H. Chung Peptide switch is essential for Sirt1 deacetylase activity Mol Cell 44 2011 203 213
48. M. Pan, H. Yuan, M. Brent, E.C. Ding, and R. Marmorstein SIRT1 contains N- and C-terminal regions that potentiate deacetylase activity J Biol Chem 287 2012 2468 2476
49. + glycohydrolase Biochemistry 47 2008 10227 10239
50. B.D. Sanders, B. Jackson, and R. Marmorstein Structural basis for sirtuin function: what we know and what we don't Biochim Biophys Acta 1804 2010 1604 1616
51. +-dependent deacetylation mechanism Proc Natl Acad Sci USA 110 2013 E2772 E2781
52. N. Blom, S. Gammeltoft, and S. Brunak Sequence and structure-based prediction of eukaryotic protein phosphorylation sites J Mol Biol 294 1999 1351 1362
53. 2 +/calmodulin-dependent kinase II Mol Cell 11 2003 1241 1251
54. E. Mossessova, and C.D. Lima Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast Mol Cell 5 2000 865 876
55. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol 276 1997 307 326
56. G.M. Sheldrick A short history of SHELX Acta Crystallogr Sect A Found Crystallogr 64 2008 112 122
57. 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
58. Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallogr Sect D Biol Crystallogr 50 1994 760 763
59. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr Sect D Biol Crystallogr 60 2004 2126 2132
60. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, and N. Echols et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr Sect D Biol Crystallogr 66 2010 213 221
61. 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
62. I.W. Davis, A. Leaver-Fay, V.B. Chen, J.N. Block, G.J. Kapral, and X. Wang et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res 35 2007 W375 W383
63. P.J. Wyatt Multiangle light scattering: the basic tool for macromolecular characterization Instrum Sci Technol 25 1997 1 18
64. 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
65. G.J. Barton ALSCRIPT: a tool to format multiple sequence alignments Protein Eng 6 1993 37 40
66. 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