The molecular basis for Histone H4- and H2A-specific amino-terminal acetylation by NatD

Structure

Volumn 23, Issue 2, 2015, Pages 332-341

  Magin, Robert S ^a,b,c   Liszczak, Glen P ^a   Marmorstein, Ronen ^a,b,d  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b WISTAR INSTITUTE   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL COENZYME A; ACYLTRANSFERASE; CARBOXYLIC ACID; CYTOCHROME C; GLYCINE; HISTONE H2A; HISTONE H4; PEPTIDE ALPHA N ACETYLTRANSFERASE D; PROTEIN VARIANT; HISTONE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CATALYSIS; CHEMICAL ANALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME SPECIFICITY; GEL FILTRATION; HISTONE ACETYLATION; HUMAN; HYDROGEN BOND; NONHUMAN; NUCLEOPHILICITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PURIFICATION; PROTEIN STRUCTURE; ACETYLATION; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; SCHIZOSACCHAROMYCES; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; STATIC ELECTRICITY;

EUKARYOTA;

ACETYLATION; AMINO ACID SEQUENCE; HISTONES; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; N-TERMINAL ACETYLTRANSFERASE D; SCHIZOSACCHAROMYCES; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY; STATIC ELECTRICITY; SUBSTRATE SPECIFICITY;

EID: 84930190696     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.10.025     Document Type: Article

References (35)

1. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, N. Echols, J.J. Headd, L.W. Hung, S. Jain, G.J. Kapral, and R.W. Grosse Kunstleve The Phenix software for automated determination of macromolecular structures Methods 55 2011 94 106
2. N. Arnaudo, I.S. Fernandez, S.H. McLaughlin, S.Y. Peak-Chew, D. Rhodes, and F. Martino The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle Nat. Struct. Mol. Biol. 20 2013 1119 1121
3. P. Emsley, B. Lohkamp, W.G. Scott, and K. Cowtan Features and development of Coot Acta Crystallogr. D Biol. Crystallogr. 66 2010 486 501
4. R. Evjenth, K. Hole, O.A. Karlsen, M. Ziegler, T. Arnesen, and J.R. Lillehaug Human Naa50p (Nat5/San) displays both protein N alpha- and N epsilon-acetyltransferase activity J. Biol. Chem. 284 2009 31122 31129
5. G.M. Forte, M.R. Pool, and C.J. Stirling N-terminal acetylation inhibits protein targeting to the endoplasmic reticulum PLoS Biol. 9 2011 e1001073
6. K. Hole, P. Van Damme, M. Dalva, H. Aksnes, N. Glomnes, J.E. Varhaug, J.R. Lillehaug, K. Gevaert, and T. Arnesen The human N-alpha-acetyltransferase 40 (hNaa40p/hNatD) is conserved from yeast and N-terminally acetylates histones H2A and H4 PLoS One 6 2011 e24713
7. S. Huang, R.C. Elliott, P.S. Liu, R.K. Koduri, J.L. Weickmann, J.H. Lee, L.C. Blair, P. Ghosh-Dastidar, R.A. Bradshaw, and K.M. Bryan Specificity of cotranslational amino-terminal processing of proteins in yeast Biochemistry 26 1987 8242 8246
8. C.S. Hwang, A. Shemorry, and A. Varshavsky N-terminal acetylation of cellular proteins creates specific degradation signals Science 327 2010 973 977
9. R.P. Jedrzejewski, and R. Kazmierkiewicz Structure of Patt1 human proapoptotic histone acetyltransferase J. Mol. Model. 19 2013 5533 5538
10. T.V. Kalvik, and T. Arnesen Protein N-terminal acetyltransferases in cancer Oncogene 32 2013 269 276
11. Y. Li, L. Zhang, T. Liu, C. Chai, Q. Fang, H. Wu, P.A. Agudelo Garcia, Z. Han, S. Zong, and Y. Yu Hat2p recognizes the histone H3 tail to specify the acetylation of the newly synthesized H3/H4 heterodimer by the Hat1p/Hat2p complex Genes Dev. 28 2014 1217 1227
12. G. Liszczak, and R. Marmorstein Implications for the evolution of eukaryotic amino-terminal acetyltransferase (NAT) enzymes from the structure of an archaeal ortholog Proc. Natl. Acad. Sci. USA 110 2013 14652 14657
13. G. Liszczak, T. Arnesen, and R. Marmorstein Structure of a ternary Naa50p (NAT5/SAN) N-terminal acetyltransferase complex reveals the molecular basis for substrate-specific acetylation J. Biol. Chem. 286 2011 37002 37010
14. G. Liszczak, J.M. Goldberg, H. Foyn, E.J. Petersson, T. Arnesen, and R. Marmorstein Molecular basis for N-terminal acetylation by the heterodimeric NatA complex Nat. Struct. Mol. Biol. 20 2013 1098 1105
15. Z. Liu, Y. Liu, H. Wang, X. Ge, Q. Jin, G. Ding, Y. Hu, B. Zhou, Z. Chen, and B. Zhang Patt1, a novel protein acetyltransferase that is highly expressed in liver and downregulated in hepatocellular carcinoma, enhances apoptosis of hepatoma cells Int. J. Biochem. Cell Biol. 41 2009 2528 2537
16. Y. Liu, D. Zhou, F. Zhang, Y. Tu, Y. Xia, H. Wang, B. Zhou, Y. Zhang, J. Wu, and X. Gao Liver Patt1 deficiency protects male mice from age-associated but not high-fat diet-induced hepatic steatosis J. Lipid Res. 53 2012 358 367
17. 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. Crystallogr. 40 2007 658 674
18. J.R. Mullen, P.S. Kayne, R.P. Moerschell, S. Tsunasawa, M. Gribskov, M. Colavito-Shepanski, M. Grunstein, F. Sherman, and R. Sternglanz Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast EMBO J. 8 1989 2067 2075
19. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Method Enzymol. 276 1997 307 326
20. B. Polevoda, and F. Sherman N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins J. Mol. Biol. 325 2003 595 622
21. B. Polevoda, J. Hoskins, and F. Sherman Properties of Nat4, an N(alpha)-acetyltransferase of Saccharomyces cerevisiae that modifies N termini of histones H2A and H4 Mol. Cell Biol. 29 2009 2913 2924
22. H.Z. Ring, V. Vameghi-Meyers, W. Wang, G.R. Crabtree, and U. Francke Five SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin (SMARC) genes are dispersed in the human genome Genomics 51 1998 140 143
23. J.R. Rojas, R.C. Trievel, J. Zhou, Y. Mo, X. Li, S.L. Berger, C.D. Allis, and R. Marmorstein Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide Nature 401 1999 93 98
24. V. Schiza, D. Molina-Serrano, D. Kyriakou, A. Hadjiantoniou, and A. Kirmizis N-alpha-terminal acetylation of histone H4 regulates arginine methylation and ribosomal DNA silencing PLoS Genet. 9 2013 e1003805
25. D.C. Scott, J.K. Monda, E.J. Bennett, J.W. Harper, and B.A. Schulman N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex Science 334 2011 674 678
26. O.K. Song, X. Wang, J.H. Waterborg, and R. Sternglanz An Nalpha-acetyltransferase responsible for acetylation of the N-terminal residues of histones H4 and H2A J. Biol. Chem. 278 2003 38109 38112
27. K.K. Starheim, K. Gevaert, and T. Arnesen Protein N-terminal acetyltransferases: when the start matters Trends Biochem. Sci. 37 2012 152 161
28. N. Stein CHAINSAW: a program for mutating pdb files used as templates in molecular replacement J. Appl. Crystallogr. 41 2008 641 643
29. P. Van Damme, K. Hole, A. Pimenta-Marques, K. Helsens, J. Vandekerckhove, R.G. Martinho, K. Gevaert, and T. Arnesen NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation PLoS Genet. 7 2011 e1002169
30. P. Van Damme, M. Lasa, B. Polevoda, C. Gazquez, A. Elosegui-Artola, D.S. Kim, E. De Juan-Pardo, K. Demeyer, K. Hole, and E. Larrea N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB Proc. Natl. Acad. Sci. USA 109 2012 12449 12454
31. M.W. Vetting, L.P. S de Carvalho, M. Yu, S.S. Hegde, S. Magnet, S.L. Roderick, and J.S. Blanchard Structure and functions of the GNAT superfamily of acetyltransferases Arch. Biochem. Biophys. 433 2005 212 226
32. Y. Yan, S. Harper, D.W. Speicher, and R. Marmorstein The catalytic mechanism of the ESA1 histone acetyltransferase involves a self-acetylated intermediate Nat. Struct. Biol. 9 2002 862 869
33. D. Yang, Q. Fang, M. Wang, R. Ren, H. Wang, M. He, Y. Sun, N. Yang, and R.M. Xu Nalpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain Nat. Struct. Mol. Biol. 20 2013 1116 1118
34. C.H. Yi, H. Pan, J. Seebacher, I.H. Jang, S.G. Hyberts, G.J. Heffron, M.G. Vander Heiden, R. Yang, F. Li, and J.W. Locasale Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survival Cell 146 2011 607 620
35. H. Yuan, and R. Marmorstein Histone acetyltransferases: rising ancient counterparts to protein kinases Biopolymers 99 2013 98 111