Structural Insights into Histone Crotonyl-Lysine Recognition by the AF9 YEATS Domain

Structure

Volumn 24, Issue 9, 2016, Pages 1606-1612

  Zhang, Qiang ^a,b   Zeng, Lei ^a,b   Zhao, Chengcheng ^a   Ju, Ying ^a   Konuma, Tsuyoshi ^b   Zhou, Ming Ming ^b  

^a JILIN UNIVERSITY   (China)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE; HISTONE ACETYL LYSINE; HISTONE H3; LYSINE; PHENYLALANINE; TYROSINE; UNCLASSIFIED DRUG; EPSILON-N-CROTONYLLYSINE; HISTONE; MLLT3 PROTEIN, HUMAN; N(ALPHA)-ACETYLLYSINE; NUCLEAR PROTEIN; PROTEIN BINDING; RECOMBINANT PROTEIN;

ACYLATION; ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; HYDROGEN BOND; HYDROPHOBICITY; ISOTHERMAL TITRATION CALORIMETRY; MOLECULAR RECOGNITION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; POINT MUTATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; ALPHA HELIX; ANALOGS AND DERIVATIVES; BETA SHEET; BINDING SITE; CHEMICAL PHENOMENA; CHEMISTRY; GENE EXPRESSION; GENETICS; HUMAN; METABOLISM; MOLECULAR CLONING; MOLECULAR MODEL; MUTATION; PROTEIN MOTIF; PROTEIN PROCESSING; X RAY CRYSTALLOGRAPHY;

AMINO ACID MOTIFS; BINDING SITES; CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; GENE EXPRESSION; HISTONES; HUMANS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LYSINE; MODELS, MOLECULAR; MUTATION; NUCLEAR PROTEINS; PHENYLALANINE; PROTEIN BINDING; PROTEIN CONFORMATION, ALPHA-HELICAL; PROTEIN CONFORMATION, BETA-STRAND; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN PROCESSING, POST-TRANSLATIONAL; RECOMBINANT PROTEINS; TYROSINE;

EID: 84985993190     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2016.05.023     Document Type: Article

References (23)

1. Andrews, F.H., Shanle, E.K., Strahl, B.D., Kutateladze, T.G., The essential role of acetyllysine binding by the YEATS domain in transcriptional regulation. Transcription 7 (2016), 14–20.
2. Andrews, F.H., Shinsky, S.A., Shanle, E.K., Bridgers, J.B., Gest, A., Tsun, I.K., Krajewski, K., Shi, X., Strahl, B.D., Kutateladze, T.G., The Taf14 YEATS domain is a reader of histone crotonylation. Nat. Chem. Biol. 12 (2016), 396–398.
3. Bao, X., Wang, Y., Li, X., Li, X.M., Liu, Z., Yang, T., Wong, C.F., Zhang, J., Hao, Q., Li, X.D., Identification of 'erasers' for lysine crotonylated histone marks using a chemical proteomics approach. Elife, 3, 2014, 10.7554/eLife.02999.
4. Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998), 905–921.
5. Clore, G.M., Gronenborn, A.M., Multidimensional heteronuclear nuclear magnetic resonance of proteins. Methods Enzymol. 239 (1994), 349–363.
6. Dai, L., Peng, C., Montellier, E., Lu, Z., Chen, Y., Ishii, H., Debernardi, A., Buchou, T., Rousseaux, S., Jin, F., et al. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat. Chem. Biol. 10 (2014), 365–370.
7. Dhalluin, C., Carlson, J.E., Zeng, L., He, C., Aggarwal, A.K., Zhou, M.M., Structure and ligand of a histone acetyltransferase bromodomain. Nature 399 (1999), 491–496.
8. Flynn, E.M., Huang, O.W., Poy, F., Oppikofer, M., Bellon, S.F., Tang, Y., Cochran, A.G., A subset of human bromodomains recognizes butyryllysine and crotonyllysine histone peptide modifications. Structure 23 (2015), 1801–1814.
9. Kouzarides, T., Chromatin modifications and their function. Cell 128 (2007), 693–705.
10. Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R., Thornton, J.M., AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8 (1996), 477–486.
11. Li, Y., Wen, H., Xi, Y., Tanaka, K., Wang, H., Peng, D., Ren, Y., Jin, Q., Dent, S.Y., Li, W., et al. AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylation. Cell 159 (2014), 558–571.
12. Li, Y., Sabari, B.R., Panchenko, T., Wen, H., Zhao, D., Guan, H., Wan, L., Huang, H., Tang, Z., Zhao, Y., et al. Molecular coupling of histone crotonylation and active transcription by AF9 YEATS domain. Mol. Cell 62 (2016), 181–193.
13. Margueron, R., Trojer, P., Reinberg, D., The key to development: interpreting the histone code?. Curr. Opin. Genet. Dev. 15 (2005), 163–176.
14. Nilges, M., O'Donoghue, S., Ambiguous NOEs and automated NOE assignment. Prog. NMR Spectrosc. 32 (1998), 107–139.
15. Ruthenburg, A.J., Li, H., Patel, D.J., Allis, C.D., Multivalent engagement of chromatin modifications by linked binding modules. Nat. Rev. Mol. Cell Biol. 8 (2007), 983–994.
16. Sabari, B.R., Tang, Z., Huang, H., Yong-Gonzalez, V., Molina, H., Kong, H.E., Dai, L., Shimada, M., Cross, J.R., Zhao, Y., et al. Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol. Cell 58 (2015), 203–215.
17. Schulze, J.M., Wang, A.Y., Kobor, M.S., YEATS domain proteins: a diverse family with many links to chromatin modification and transcription. Biochem. Cell Biol. 87 (2009), 65–75.
18. Shanle, E.K., Andrews, F.H., Meriesh, H., McDaniel, S.L., Dronamraju, R., DiFiore, J.V., Jha, D., Wozniak, G.G., Bridgers, J.B., Kerschner, J.L., et al. Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response. Genes Dev. 29 (2015), 1795–1800.
19. Smith, S.G., Zhou, M.M., The bromodomain: a new target in emerging epigenetic medicine. ACS Chem. Biol. 11 (2016), 598–608.
20. Tan, M., Luo, H., Lee, S., Jin, F., Yang, J.S., Montellier, E., Buchou, T., Cheng, Z., Rousseaux, S., Rajagopal, N., et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146 (2011), 1016–1028.
21. Zeng, L., Zhou, M.M., Bromodomain: an acetyl-lysine binding domain. FEBS Lett. 513 (2002), 124–128.
22. Zeng, L., Zhang, Q., Li, S., Plotnikov, A.N., Walsh, M.J., Zhou, M.-M., Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature 466 (2010), 258–262.
23. Zhao, D., Guan, H., Zhao, S., Mi, W., Wen, H., Li, Y., Zhao, Y., Allis, C.D., Shi, X., Li, H., YEATS2 is a selective histone crotonylation reader. Cell Res. 26 (2016), 629–632.