Structural basis of histone demethylation by LSD1 revealed by suicide inactivation

Nature Structural and Molecular Biology

Volumn 14, Issue 6, 2007, Pages 535-539

  Yang, Maojun ^a   Culhane, Jeffrey C ^b   Szewczuk, Lawrence M ^b   Gocke, Christian B ^a   Brautigam, Chad A ^c   Tomchick, Diana R ^c   MacHius, Mischa ^c   Cole, Philip A ^b   Yu, Hongtao ^a  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; ISOENZYME; LYSINE; PROTEIN LSD1; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CATALYSIS; COVALENT BOND; CRYSTAL STRUCTURE; DEMETHYLATION; ENZYME CONFORMATION; ENZYME INACTIVATION; ENZYME SPECIFICITY; ENZYME STRUCTURE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; STRUCTURAL PROTEOMICS;

AMINO ACID SEQUENCE; CRYSTALLIZATION; GENE SILENCING; HISTONES; HUMANS; METHYLATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; MUTAGENESIS; OXIDOREDUCTASES, N-DEMETHYLATING; SUBSTRATE SPECIFICITY;

EID: 34249881352     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1255     Document Type: Article

References (27)

1. Martin, C. & Zhang, Y. The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 6, 838-849 (2005).
2. Ruthenburg, A.J., Allis, C.D. & Wysocka, J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell 25, 15-30 (2007).
3. Shi, Y. et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941-953 (2004).
4. Shi, Y. & Whetstine, J.R. Dynamic regulation of histone lysine methylation by demethylases. Mol. Cell 25, 1-14 (2007).
5. Metzger, E. et al. LSD1 demethylates repressive histone marks to promote androgenreceptor-dependent transcription. Nature 437, 436-439 (2005).
6. Wissmann, M. et al. Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression. Nat. Cell Biol. 9, 347-353 (2007).
7. Garcia-Bassets, I. et al. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell 128, 505-518 (2007).
8. Yang, M. et al. Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Mol. Cell 23, 377-387 (2006).
9. Stavropoulos, P., Blobel, G. & Hoelz, A. Crystal structure and mechanism of human lysine-specific demethylase-1. Nat. Struct. Mol. Biol. 13, 626-632 (2006).
10. Chen, Y. et al. Crystal structure of human histone lysine-specific demethylase 1 (LSD1). Proc. Natl. Acad. Sci. USA 103, 13956-13961 (2006).
11. Banerjee, A., Yang, W., Karplus, M. & Verdine, G.L. Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434, 612-618 (2005).
12. Zhang, X., Gureasko, J., Shen, K., Cole, P.A. & Kuriyan, J. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell 125, 1137-1149 (2006).
13. Culhane, J.C. et al. A mechanism-based inactivator for histone demethylase LSD1. J. Am. Chem. Soc. 128, 4536-4537 (2006).
14. Szewczuk, L.M. et al. Mechanistic analysis of a suicide inactivator of histone demethylase LSD1. Biochemistry (in the press).
15. Forneris, F., Binda, C., Vanoni, M.A., Battaglioli, E. & Mattevi, A. Human histone demethylase LSD1 reads the histone code. J. Biol. Chem. 280, 41360-41365 (2005).
16. Zhang, X. et al. Structural basis for the product specificity of histone lysine methyltransferases. Mol. Cell 12, 177-185 (2003).
17. Hakimi, M.A., Dong, Y., Lane, W.S., Speicher, D.W. & Shiekhattar, R. A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. J. Biol. Chem. 278, 7234-7239 (2003).
18. Humphrey, G.W. et al. Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1. J. Biol. Chem. 276, 6817-6824 (2001).
19. Shi, Y. et al. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature 422, 735-738 (2003).
20. Lee, M.G. et al. Functional interplay between histone demethylase and deacetylase enzymes. Mol. Cell. Biol. 26, 6395-6402 (2006).
21. Bolden, J.E., Peart, M.J. & Johnstone, R.W. Anticancer activities of histone deacetylase inhibitors. Nat. Rev. Drug Discov. 5, 769-784 (2006).
22. Otwinowski, Z. & Minor, W. Processing X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
23. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255 (1997).
24. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763 (1994).
25. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132 (2004).
26. Lovell, S.C. et al. Structure validation by Cα geometry: Φ,ψ and Cβ deviation. Proteins 50, 437-450 (2003).
27. Brünger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921 (1998).