1cm0 Citations

Crystal structure of the histone acetyltransferase domain of the human PCAF transcriptional regulator bound to coenzyme A.

EMBO J 18 3521-32 (1999)
Cited: 90 times
EuropePMC logo PMID: 10393169

Abstract

The human p300/CBP-associating factor, PCAF, mediates transcriptional activation through its ability to acetylate nucleosomal histone substrates as well as transcriptional activators such as p53. We have determined the 2.3 A crystal structure of the histone acetyltransferase (HAT) domain of PCAF bound to coenzyme A. The structure reveals a central protein core associated with coenzyme A binding and a pronounced cleft that sits over the protein core and is flanked on opposite sides by the N- and C-terminal protein segments. A correlation of the structure with the extensive mutagenesis data for PCAF and the homologous yeast GCN5 protein implicates the cleft and the N- and C-terminal protein segments as playing an important role in histone substrate binding, and a glutamate residue in the protein core as playing an essential catalytic role. A structural comparison with the coenzyme-bound forms of the related N-acetyltransferases, HAT1 (yeast histone acetyltransferase 1) and SmAAT (Serratia marcescens aminoglycoside 3-N-acetyltransferase), suggests the mode of substrate binding and catalysis by these enzymes and establishes a paradigm for understanding the structure-function relationships of other enzymes that acetylate histones and transcriptional regulators to promote activated transcription.

Reviews - 1cm0 mentioned but not cited (6)

  1. Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT). Salah Ud-Din AI, Tikhomirova A, Roujeinikova A. Int J Mol Sci 17 E1018 (2016)
  2. Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives. Andreoli F, Barbosa AJ, Parenti MD, Del Rio A. Curr Pharm Des 19 578-613 (2013)
  3. Mammalian N-acetylglutamate synthase. Morizono H, Caldovic L, Shi D, Tuchman M. Mol Genet Metab 81 Suppl 1 S4-11 (2004)
  4. The Ada2/Ada3/Gcn5/Sgf29 histone acetyltransferase module. Espinola-Lopez JM, Tan S. Biochim Biophys Acta Gene Regul Mech 1864 194629 (2021)
  5. Regulation of Thermogenic Adipocyte Differentiation and Adaptive Thermogenesis Through Histone Acetylation. Ong BX, Brunmeir R, Zhang Q, Peng X, Idris M, Liu C, Xu F. Front Endocrinol (Lausanne) 11 95 (2020)
  6. The Biological Significance of Targeting Acetylation-Mediated Gene Regulation for Designing New Mechanistic Tools and Potential Therapeutics. O'Garro C, Igbineweka L, Ali Z, Mezei M, Mujtaba S. Biomolecules 11 455 (2021)

Articles - 1cm0 mentioned but not cited (5)

  1. Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. Lasko LM, Jakob CG, Edalji RP, Qiu W, Montgomery D, Digiammarino EL, Hansen TM, Risi RM, Frey R, Manaves V, Shaw B, Algire M, Hessler P, Lam LT, Uziel T, Faivre E, Ferguson D, Buchanan FG, Martin RL, Torrent M, Chiang GG, Karukurichi K, Langston JW, Weinert BT, Choudhary C, de Vries P, Van Drie JH, McElligott D, Kesicki E, Marmorstein R, Sun C, Cole PA, Rosenberg SH, Michaelides MR, Lai A, Bromberg KD. Nature 550 128-132 (2017)
  2. X-ray structure of the AAC(6')-Ii antibiotic resistance enzyme at 1.8 A resolution; examination of oligomeric arrangements in GNAT superfamily members. Burk DL, Ghuman N, Wybenga-Groot LE, Berghuis AM. Protein Sci 12 426-437 (2003)
  3. Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family. Tyler RC, Bitto E, Berndsen CE, Bingman CA, Singh S, Lee MS, Wesenberg GE, Denu JM, Phillips GN, Markley JL. Biochemistry 45 14325-14336 (2006)
  4. Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface. Shirmast P, Ghafoori SM, Irwin RM, Abendroth J, Mayclin SJ, Lorimer DD, Edwards TE, Forwood JK. Sci Rep 11 1274 (2021)
  5. Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate. Bottoms CA, Xu D. BMC Bioinformatics 9 Suppl 9 S16 (2008)


Reviews citing this publication (23)

  1. Histone acetyltransferases. Roth SY, Denu JM, Allis CD. Annu Rev Biochem 70 81-120 (2001)
  2. Acetylation of histones and transcription-related factors. Sterner DE, Berger SL. Microbiol Mol Biol Rev 64 435-459 (2000)
  3. 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond. Verdin E, Ott M. Nat Rev Mol Cell Biol 16 258-264 (2015)
  4. Structure and functions of the GNAT superfamily of acetyltransferases. Vetting MW, S de Carvalho LP, Yu M, Hegde SS, Magnet S, Roderick SL, Blanchard JS. Arch Biochem Biophys 433 212-226 (2005)
  5. GCN5-related N-acetyltransferases: a structural overview. Dyda F, Klein DC, Hickman AB. Annu Rev Biophys Biomol Struct 29 81-103 (2000)
  6. Writers and readers of histone acetylation: structure, mechanism, and inhibition. Marmorstein R, Zhou MM. Cold Spring Harb Perspect Biol 6 a018762 (2014)
  7. Distinct GCN5/PCAF-containing complexes function as co-activators and are involved in transcription factor and global histone acetylation. Nagy Z, Tora L. Oncogene 26 5341-5357 (2007)
  8. Histone acetyltransferases: function, structure, and catalysis. Marmorstein R, Roth SY. Curr Opin Genet Dev 11 155-161 (2001)
  9. Chemistry of acetyl transfer by histone modifying enzymes: structure, mechanism and implications for effector design. Hodawadekar SC, Marmorstein R. Oncogene 26 5528-5540 (2007)
  10. Epigenetics--an epicenter of gene regulation: histones and histone-modifying enzymes. Biel M, Wascholowski V, Giannis A. Angew Chem Int Ed Engl 44 3186-3216 (2005)
  11. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Ali I, Conrad RJ, Verdin E, Ott M. Chem Rev 118 1216-1252 (2018)
  12. Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress. Hentchel KL, Escalante-Semerena JC. Microbiol Mol Biol Rev 79 321-346 (2015)
  13. Protein modules that manipulate histone tails for chromatin regulation. Marmorstein R. Nat Rev Mol Cell Biol 2 422-432 (2001)
  14. Structure of histone acetyltransferases. Marmorstein R. J Mol Biol 311 433-444 (2001)
  15. Strategies for manipulating the p53 pathway in the treatment of human cancer. Hupp TR, Lane DP, Ball KL. Biochem J 352 Pt 1 1-17 (2000)
  16. Control of histone modifications. Davie JR, Spencer VA. J Cell Biochem Suppl 32-33 141-148 (1999)
  17. An evolving understanding of nuclear receptor coregulator proteins. Millard CJ, Watson PJ, Fairall L, Schwabe JW. J Mol Endocrinol 51 T23-36 (2013)
  18. Histone acetyltransferase inhibitors and preclinical studies. Manzo F, Tambaro FP, Mai A, Altucci L. Expert Opin Ther Pat 19 761-774 (2009)
  19. Histone Lysine and Genomic Targets of Histone Acetyltransferases in Mammals. Voss AK, Thomas T. Bioessays 40 e1800078 (2018)
  20. Structure and mechanism of non-histone protein acetyltransferase enzymes. Friedmann DR, Marmorstein R. FEBS J 280 5570-5581 (2013)
  21. Small molecule inhibitors of histone acetyltransferases as epigenetic tools and drug candidates. Furdas SD, Kannan S, Sippl W, Jung M. Arch Pharm (Weinheim) 345 7-21 (2012)
  22. Revisiting Histone Deacetylases in Human Tumorigenesis: The Paradigm of Urothelial Bladder Cancer. Giannopoulou AF, Velentzas AD, Konstantakou EG, Avgeris M, Katarachia SA, Papandreou NC, Kalavros NI, Mpakou VE, Iconomidou V, Anastasiadou E, Kostakis IK, Papassideri IS, Voutsinas GE, Scorilas A, Stravopodis DJ. Int J Mol Sci 20 E1291 (2019)
  23. Writing and rewriting the epigenetic code of cancer cells: from engineered proteins to small molecules. Blancafort P, Jin J, Frye S. Mol Pharmacol 83 563-576 (2013)

Articles citing this publication (56)

  1. The language of covalent histone modifications. Strahl BD, Allis CD. Nature 403 41-45 (2000)
  2. Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Ikura T, Ogryzko VV, Grigoriev M, Groisman R, Groisman R, Wang J, Horikoshi M, Scully R, Qin J, Nakatani Y. Cell 102 463-473 (2000)
  3. Retinoic acid receptors: from molecular mechanisms to cancer therapy. di Masi A, Leboffe L, De Marinis E, Pagano F, Cicconi L, Rochette-Egly C, Lo-Coco F, Ascenzi P, Nervi C. Mol Aspects Med 41 1-115 (2015)
  4. Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide. Rojas JR, Trievel RC, Zhou J, Mo Y, Li X, Berger SL, Allis CD, Marmorstein R. Nature 401 93-98 (1999)
  5. Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites. Parris KD, Lin L, Tam A, Mathew R, Hixon J, Stahl M, Fritz CC, Seehra J, Somers WS. Structure 8 883-895 (2000)
  6. Crystal structure of yeast Esa1 suggests a unified mechanism for catalysis and substrate binding by histone acetyltransferases. Yan Y, Barlev NA, Haley RH, Berger SL, Marmorstein R. Mol Cell 6 1195-1205 (2000)
  7. Characterization of histone acylations links chromatin modifications with metabolism. Simithy J, Sidoli S, Yuan ZF, Coradin M, Bhanu NV, Marchione DM, Klein BJ, Bazilevsky GA, McCullough CE, Magin RS, Kutateladze TG, Snyder NW, Marmorstein R, Garcia BA. Nat Commun 8 1141 (2017)
  8. Catalytic mechanism of a MYST family histone acetyltransferase. Berndsen CE, Albaugh BN, Tan S, Denu JM. Biochemistry 46 623-629 (2007)
  9. MCM3AP, a novel acetyltransferase that acetylates replication protein MCM3. Takei Y, Swietlik M, Tanoue A, Tsujimoto G, Kouzarides T, Laskey R. EMBO Rep 2 119-123 (2001)
  10. Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM. Genes Dev 33 1751-1774 (2019)
  11. Cyclin D1 Is a Ligand-independent Co-repressor for Thyroid Hormone Receptors. Lin HM, Zhao L, Cheng SY. J Biol Chem 277 28733-28741 (2002)
  12. Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor. Poux AN, Cebrat M, Kim CM, Cole PA, Marmorstein R. Proc Natl Acad Sci U S A 99 14065-14070 (2002)
  13. Application of a fluorescent histone acetyltransferase assay to probe the substrate specificity of the human p300/CBP-associated factor. Trievel RC, Li FY, Marmorstein R. Anal Biochem 287 319-328 (2000)
  14. The histone acetyltransferase PCAF regulates p21 transcription through stress-induced acetylation of histone H3. Love IM, Sekaric P, Shi D, Grossman SR, Androphy EJ. Cell Cycle 11 2458-2466 (2012)
  15. Glucagon regulates gluconeogenesis through KAT2B- and WDR5-mediated epigenetic effects. Ravnskjaer K, Hogan MF, Lackey D, Tora L, Dent SY, Olefsky J, Montminy M. J Clin Invest 123 4318-4328 (2013)
  16. Sas3 is a histone acetyltransferase and requires a zinc finger motif. Takechi S, Nakayama T. Biochem Biophys Res Commun 266 405-410 (1999)
  17. Functional analysis of the p300 acetyltransferase domain: the PHD finger of p300 but not of CBP is dispensable for enzymatic activity. Bordoli L, Hüsser S, Lüthi U, Netsch M, Osmani H, Eckner R. Nucleic Acids Res 29 4462-4471 (2001)
  18. The human histone acetyltransferase P/CAF is a promiscuous histone propionyltransferase. Leemhuis H, Packman LC, Nightingale KP, Hollfelder F. Chembiochem 9 499-503 (2008)
  19. Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for beta-lactam acetylation. He H, Ding Y, Bartlam M, Sun F, Le Y, Qin X, Tang H, Zhang R, Joachimiak A, Liu J, Zhao N, Rao Z. J Mol Biol 325 1019-1030 (2003)
  20. Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography. Sakamoto K, Murayama K, Oki K, Iraha F, Kato-Murayama M, Takahashi M, Ohtake K, Kobayashi T, Kuramitsu S, Shirouzu M, Yokoyama S. Structure 17 335-344 (2009)
  21. Multiple lysine methylation of PCAF by Set9 methyltransferase. Masatsugu T, Yamamoto K. Biochem Biophys Res Commun 381 22-26 (2009)
  22. Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1. Wu H, Moshkina N, Min J, Zeng H, Joshua J, Zhou MM, Plotnikov AN. Proc Natl Acad Sci U S A 109 8925-8930 (2012)
  23. Modulating acetyl-CoA binding in the GCN5 family of histone acetyltransferases. Langer MR, Fry CJ, Peterson CL, Denu JM. J Biol Chem 277 27337-27344 (2002)
  24. Atomic resolution structure of human α-tubulin acetyltransferase bound to acetyl-CoA. Taschner M, Taschner M, Vetter M, Lorentzen E. Proc Natl Acad Sci U S A 109 19649-19654 (2012)
  25. Crystal structure of a binary complex between human GCN5 histone acetyltransferase domain and acetyl coenzyme A. Schuetz A, Bernstein G, Dong A, Antoshenko T, Wu H, Loppnau P, Bochkarev A, Plotnikov AN. Proteins 68 403-407 (2007)
  26. T:G mismatch-specific thymine-DNA glycosylase (TDG) as a coregulator of transcription interacts with SRC1 family members through a novel tyrosine repeat motif. Lucey MJ, Chen D, Lopez-Garcia J, Hart SM, Phoenix F, Al-Jehani R, Alao JP, White R, Kindle KB, Losson R, Chambon P, Parker MG, Schär P, Heery DM, Buluwela L, Ali S. Nucleic Acids Res 33 6393-6404 (2005)
  27. Acetyltransferase machinery conserved in p300/CBP-family proteins. Yuan LW, Giordano A. Oncogene 21 2253-2260 (2002)
  28. Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2. Sun J, Paduch M, Kim SA, Kramer RM, Barrios AF, Lu V, Luke J, Usatyuk S, Kossiakoff AA, Tan S. Proc Natl Acad Sci U S A 115 10010-10015 (2018)
  29. Influenza A virus nucleoprotein is acetylated by histone acetyltransferases PCAF and GCN5. Hatakeyama D, Shoji M, Yamayoshi S, Yoh R, Ohmi N, Takenaka S, Saitoh A, Arakaki Y, Masuda A, Komatsu T, Nagano R, Nakano M, Noda T, Kawaoka Y, Kuzuhara T. J Biol Chem 293 7126-7138 (2018)
  30. Inhibition of the PCAF histone acetyl transferase and cell proliferation by isothiazolones. Dekker FJ, Ghizzoni M, van der Meer N, Wisastra R, Haisma HJ. Bioorg Med Chem 17 460-466 (2009)
  31. Histone H3 Ser10 phosphorylation-independent function of Snf1 and Reg1 proteins rescues a gcn5- mutant in HIS3 expression. Liu Y, Xu X, Singh-Rodriguez S, Zhao Y, Kuo MH. Mol Cell Biol 25 10566-10579 (2005)
  32. Primers on chromatin. Lall S. Nat Struct Mol Biol 14 1110-1115 (2007)
  33. FeeM, an N-acyl amino acid synthase from an uncultured soil microbe: structure, mechanism, and acyl carrier protein binding. Van Wagoner RM, Clardy J. Structure 14 1425-1435 (2006)
  34. Snf1p regulates Gcn5p transcriptional activity by antagonizing Spt3p. Liu Y, Xu X, Kuo MH. Genetics 184 91-105 (2010)
  35. Cloning and analysis of a Toxoplasma gondii histone acetyltransferase: a novel chromatin remodelling factor in Apicomplexan parasites. Hettmann C, Soldati D. Nucleic Acids Res 27 4344-4352 (1999)
  36. PCAF-Mediated Histone Acetylation Promotes Replication Fork Degradation by MRE11 and EXO1 in BRCA-Deficient Cells. Kim JJ, Lee SY, Choi JH, Woo HG, Xhemalce B, Miller KM. Mol Cell 80 327-344.e8 (2020)
  37. Acetyltransferase p300/CBP associated Factor (PCAF) regulates crosstalk-dependent acetylation of histone H3 by distal site recognition. Kornacki JR, Stuparu AD, Mrksich M. ACS Chem Biol 10 157-164 (2015)
  38. Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthesis. Hung MN, Rangarajan E, Munger C, Nadeau G, Sulea T, Matte A. J Bacteriol 188 5606-5617 (2006)
  39. Targeting of histone acetyltransferase p300 by cyclopentenone prostaglandin Δ(12)-PGJ(2) through covalent binding to Cys(1438). Ravindra KC, Narayan V, Lushington GH, Peterson BR, Prabhu KS. Chem Res Toxicol 25 337-347 (2012)
  40. Structure of a bacterial toxin-activating acyltransferase. Greene NP, Crow A, Hughes C, Koronakis V. Proc Natl Acad Sci U S A 112 E3058-66 (2015)
  41. Human protein N-terminal acetyltransferase hNaa50p (hNAT5/hSAN) follows ordered sequential catalytic mechanism: combined kinetic and NMR study. Evjenth RH, Brenner AK, Thompson PR, Arnesen T, Frøystein NÅ, Lillehaug JR. J Biol Chem 287 10081-10088 (2012)
  42. Dimeric structure of p300/CBP associated factor. Shi S, Lin J, Cai Y, Yu J, Hong H, Ji K, Downey JS, Lu X, Chen R, Han J, Han A. BMC Struct Biol 14 2 (2014)
  43. Identification of epigenetic factor KAT2B gene variants for possible roles in congenital heart diseases. Hou YS, Wang JZ, Shi S, Han Y, Zhang Y, Zhi JX, Xu C, Li FF, Wang GY, Liu SL. Biosci Rep 40 BSR20191779 (2020)
  44. De novo discovery of serotonin N-acetyltransferase inhibitors. Szewczuk LM, Saldanha SA, Ganguly S, Bowers EM, Javoroncov M, Karanam B, Culhane JC, Holbert MA, Klein DC, Abagyan R, Cole PA. J Med Chem 50 5330-5338 (2007)
  45. Involvement of Hat1p (Kat1p) catalytic activity and subcellular localization in telomeric silencing. Mersfelder EL, Parthun MR. J Biol Chem 283 29060-29068 (2008)
  46. Crystal structure of Bacillus subtilis YdaF protein: a putative ribosomal N-acetyltransferase. Brunzelle JS, Wu R, Korolev SV, Collart FR, Joachimiak A, Anderson WF. Proteins 57 850-853 (2004)
  47. Modulating substrate specificity of histone acetyltransferase with unnatural amino acids. Mehta KR, Yang CY, Montclare JK. Mol Biosyst 7 3050-3055 (2011)
  48. PanM, an acetyl-coenzyme A sensor required for maturation of L-aspartate decarboxylase (PanD). Stuecker TN, Tucker AC, Escalante-Semerena JC. mBio 3 e00158-12 (2012)
  49. Structural Basis of Eco1-Mediated Cohesin Acetylation. Chao WC, Wade BO, Bouchoux C, Jones AW, Purkiss AG, Federico S, O'Reilly N, Snijders AP, Uhlmann F, Singleton MR. Sci Rep 7 44313 (2017)
  50. Directed evolution of a histone acetyltransferase--enhancing thermostability, whilst maintaining catalytic activity and substrate specificity. Leemhuis H, Nightingale KP, Hollfelder F. FEBS J 275 5635-5647 (2008)
  51. Competitive Inhibition of Lysine Acetyltransferase 2B by a Small Motif of the Adenoviral Oncoprotein E1A. Shi S, Liu K, Chen Y, Zhang S, Lin J, Gong C, Jin Q, Yang XJ, Chen R, Ji Z, Han A. J Biol Chem 291 14363-14372 (2016)
  52. Identification of amino acid residues essential for the yeast N-acetyltransferase Mpr1 activity by site-directed mutagenesis. Kotani T, Takagi H. FEMS Yeast Res 8 607-614 (2008)
  53. KAT2B Gene Polymorphisms Are Associated with Body Measure Traits in Four Chinese Cattle Breeds. Lin X, Li B, Chen Y, Chen H, Liu M. Animals (Basel) 12 1954 (2022)
  54. Complementary PCAF-coenzyme A mutagenesis: chemoenzymatic synthesis of a novel enlarged coenzyme A analogue and evaluation of its biological activity. Khim L, Han J, Willetts L, Brady K, Gillece P, Rached O, Thomas NR, Stylianou E. Chembiochem 11 2100-2103 (2010)
  55. Azide-alkyne cycloaddition affording enzymatically tunable bisubstrate based inhibitors of histone acetyltransferase PCAF. van Ameijde J, Zwiebel AP, Ruijtenbeek R, Liskamp RM. Bioorg Med Chem Lett 24 113-116 (2014)
  56. Genome-wide identification, phylogenetic classification of histone acetyltransferase genes, and their expression analysis in sugar beet (Beta vulgaris L.) under salt stress. Yolcu S, Skorupa M, Uras ME, Mazur J, Ozyiğit II. Planta 259 85 (2024)