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Crystal structure and mechanism of human lysine-specific demethylase-1

Nature Structural & Molecular Biology volume 13, pages 626–632 (2006)Cite this article

Abstract

The reversible methylation of specific lysine residues in histone tails is crucial in epigenetic gene regulation. LSD1, the first known lysine-specific demethylase, selectively removes monomethyl and dimethyl, but not trimethyl modifications of Lys4 or Lys9 of histone-3. Here, we present the crystal structure of LSD1 at 2.9-Å resolution. LSD1 forms a highly asymmetric, closely packed domain structure from which a long helical 'tower' domain protrudes. The active site cavity is spacious enough to accommodate several residues of the histone tail substrate, but does not appear capable of recognizing the different methylation states of the substrate lysine. This supports the hypothesis that trimethylated lysine is chemically rather than sterically discriminated. We present a biochemical analysis of LSD1 mutants that identifies crucial residues in the active site cavity and shows the importance of the SWIRM and tower domains for catalysis.

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Figure 1: Structure of human LSD1.
Figure 2: Structure of the SWIRM domain of LSD1.
Figure 3: Structure of the oxidase domain and active site cavity of LSD1.
Figure 4: Allosteric regulation of LSD1.
Figure 5: Initial velocities of LSD1 mutants.

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Acknowledgements

We thank the Kazusa DNA Research Institute for the complementary DNA clone of human LSD1, C. Ralston for invaluable support during data collection at the Advanced Light Source, K. Heyman for technical support, A. Patke for discussions, S. Lawrie and S. Etherton for help with editing the manuscript and members of the Blobel laboratory for discussions and comments on the manuscript. N-terminal protein sequencing and peptide synthesis were performed by the Protein Center of the Rockefeller University, and multiangle light-scattering analysis was carried out by the Yale Proteomics Facility. A.H. was supported by a grant from the Leukemia and Lymphoma Society.

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  1. Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, 10021, New York, USA

    Pete Stavropoulos, Günter Blobel & André Hoelz

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  1. Pete Stavropoulos
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  2. Günter Blobel
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  3. André Hoelz
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Contributions

P.S. and A.H. designed and performed experiments; P.S., G.B. and A.H. analyzed and interpreted data; A.H. prepared the figures and the manuscript.

Note: Supplementary information is available on the Nature Structural & Molecular Biology website.

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Correspondence to André Hoelz.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Sequence alignment of LSD1 homologs (PDF 219 kb)

Supplementary Fig. 2

Electron density maps (PDF 5025 kb)

Supplementary Fig. 3

The SWIRM domain of LSD1 (PDF 251 kb)

Supplementary Fig. 4

Trimethylated H3-K4 peptide acts as a competitive inhibitor of LSD1 activity (PDF 50 kb)

Supplementary Table 1

Biochemical analysis of LSD1 mutants (PDF 477 kb)

Supplementary Table 2

Crystallographic analysis (PDF 461 kb)

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Stavropoulos, P., Blobel, G. & Hoelz, A. Crystal structure and mechanism of human lysine-specific demethylase-1. Nat Struct Mol Biol 13, 626–632 (2006). https://doi.org/10.1038/nsmb1113

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