Crystal structure of the histone lysine specific demethylase LSD1 complexed with tetrahydrofolate

Protein Science

Volumn 23, Issue 7, 2014, Pages 993-998

  Luka, Zigmund ^a   Pakhomova, Svetlana ^b   Loukachevitch, Lioudmila V ^a   Calcutt, M Wade ^a   Newcomer, Marcia E ^b   Wagner, Conrad ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

Crystal structure; Epigenetics; LSD1; Tetrahydrofolate

Indexed keywords

CO REPRESSOR FOR REPRESSOR ELEMENT 1 SILENCING TRANSCRIPTION FACTOR; FLAVINE ADENINE NUCLEOTIDE; FOLIC ACID; HISTONE DEMETHYLASE; LYSINE SPECIFIC DEMETHYLASE 1; TETRAHYDROFOLIC ACID; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; COREPRESSOR PROTEIN; LYSINE; TETRAHYDROFOLIC ACID DERIVATIVE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CRYSTAL STRUCTURE; DEMETHYLATION; ENZYME ACTIVITY; ENZYME MECHANISM; IN VITRO STUDY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; HUMAN; METABOLISM; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CO-REPRESSOR PROTEINS; CRYSTALLOGRAPHY, X-RAY; FLAVIN-ADENINE DINUCLEOTIDE; HISTONE DEMETHYLASES; HUMANS; LYSINE; MASS SPECTROMETRY; MODELS, MOLECULAR; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY; TETRAHYDROFOLATES;

EID: 84904204533     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2469     Document Type: Article

References (21)

1. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941-953.
2. Forneris F, Binda C, Vanoni MA, Mattevi A, Battaglioli E (2005) Histone demethylation catalysed by LSD1 is a flavin-dependent oxidative process. FEBS Lett 579: 2203-2207.
3. Culhane JC, Cole PA (2007) LSD1 and the chemistry of histone demethylation. Curr Opin Chem Biol 11:561-568.
4. Anand R, Marmorstein R (2007) Structure and mechanism of lysine-specific demethylase enzymes. J Biol Chem 282:35425-35429.
5. Lan F, Nottke AC, Shi Y (2008) Mechanisms involved in the regulation of histone lysine demethylases. Curr Opin Cell Biol 20:316-325.
6. Wittwer AJ, Wagner C (1981) Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Purification and folate-binding characteristics. J Biol Chem 256:4102-4108.
7. Wittwer AJ, Wagner C (1981) Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Flavoprotein nature and enzymatic properties of the purified proteins. J Biol Chem 256:4109-4115.
8. Luka Z, Moss F, Loukachevitch LV, Bornhop DJ, Wagner C (2011) Histone demethylase LSD1 is a folate-binding protein. Biochemistry 50:4750-4756.
9. Yang M, Gocke CB, Luo X, Borek D, Tomchick DR, Machius M, Otwinowski Z, Yu H (2006) Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. Mol Cell 23:377-387.
10. Forneris F, Binda C, Adamo A, Battaglioli E, Mattevi A (2007) Structural basis of LSD1-CoREST selectivity in histone H3 recognition. J Biol Chem 282:20070-20074.
11. Poe M, Benkovic SJ (1980) 5-Formyl- and 10-formyl- 5,6,7,8- tetrahydrofolate. Conformation of the tetrahydropyrazine ring and formyl group in solution. Biochemistry 19:4576-4582.
12. Matthews DA, Alden RA, Bolin JT, Freer ST, Hamlin R, Xuong N, Kraut J, Poe M, Williams M, Hoogsteen K (1977) Dihydrofolate reductase: X-ray structure of the binary complex with methotrexate. Science 197:452-455.
13. Luka Z, Pakhomova S, Loukachevitch LV, Egli M, Newcomer ME, Wagner C (2006) 5-Methyltetrahydrofolate is bound in intersubunit areas of rat liver folatebinding protein glycine N-methyltransferase. J Biol Chem 282:4069-4075.
14. Wallace AC, Laskowski RA, Thornton JM (1996) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8:127-134.
15. Blakley RL (1958) Interaction of formaldehyde and tetrahydrofolic acid and its relation to the enzymic synthesis of serine. Nature 182:1719-1722.
16. Kallen RG, Jencks WP (1966) The mechanism of the condensation of formaldehyde with tetrahydrofolic acid. J Biol Chem 241:5851-5863.
17. Stover PJ, Field MS (2011) Trafficking of intracellular folates. Adv Nutr 2:325-331.
18. Otwinowski Z, Minor W, Processing of X-ray diffraction data collected in oscillation mode. In: Carter CW Jr, Sweet RM, Eds. (1997) Methods in enzymology, Vol. 276: Macromolecular crystallography, Part A. New York: Academic Press, pp 307-326.
19. Bailey S (1994) The Ccp4 suite-programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50: 760-763.
20. Painter J, Merritt EA (2006) TLSMD web server for the generation of multi-group TLS models. J Appl Crystallogr 39:109-111.
21. Emsley P, Lohkamp B, Scott W, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486-501.