Protein Name

Lysine-Specific Demethylase-1


Homo sapiens (human)

Biological Context

Eukaryotic cells use histones to compact DNA and to compose a chromatin structure. The flexible N-terminal histone tails are the sites for a variety of chemical modifications that alter the interaction between histones and DNA, and thus are necessary for epigenetic gene regulation.

LSD1, the first known lysine-specific demethylase, selectively removes monomethyl and dimethyl, but not trimethyl modifications of the Lys4 or Lys9 of histone-3. LSD1 is found in histone complexes and regulates cell-specific gene expression. Combinations between LSD1 and its inhibitor proteins like BHC80, have a crucial role in both gene repression and gene activation.

Structure Description


The crystal structure shown here is of the LSD1 complexed with cofactor FAD. The LSD1 polypeptide chain can be mainly divided into 3 regions: SWIRM domain, oxidase domain and tower domain. The N-terminal SWIRM domain and the C-terminal oxidase domain closely pack against each other via hydrophobic interactions to form a core structure from which the tower domain protrudes (Fig. 1).

The SWIRM domain is found in a number of proteins involved in chromatin remodeling and histone modification and has a DNA binding ability. However, in contrast to other SWIRM domains, the residues for DNA binding are not conserved in LSD1 and thus a low capability for DNA binding is assumed. On the contrary, the residues on the interface involved in oxidase domain binding are essentially invariant across species, and a series of mutant experiments showed the importance of a cleft in the interface to the catalytic site. This cleft may engage the histone tail substrate, and show the necessity of the SWIRM domain for catalysis.

The oxidase domain consists of two functional lobes, substrate-binding and FAD-binding ones. The substrate-binding lobe has a large active site cavity (Fig. 2) that can bind not only the substrate lysine but also several adjacent residues. Because of the cavity size, a trimethylated lysine can also enter it. So it is difficult to distinguish trimethylated lysines from mono- and dimethylated ones sterically, and chemical discrimination is therefore supposed.

The tower domain formed by two long α-helices connects to the substrate-binding lobe of the oxidase domain. So, the binding of other proteins to the tower domain may potentially regulate the size of the active site cavity. Besides, a tower-less mutant has greatly reduced catalytic activity. Thus, the tower domain may act as a molecular lever that allosterically regulates the catalytic activity of LSD1.

This structure and mutant experiments show the importance of the SWIRM and tower domains for catalysis within the oxidase domain. Further analysis for LSD1-histone tail complexes and investigation of methylated-specific recognition mechanisms are expected.

2H94_structure (Fig. 1) Structure of human LSD1

Yellow, SWIRM domain; blue, oxidase domain; green, tower domain.
2H94_surface (Fig. 2) Surface of human LSD1

Yellow, SWIRM domain; blue, oxidase domain; green, tower domain.The oxidase domain has a large active site cavity.

Protein Data Bank (PDB)



Stavropoulos, P. Blobel, G. Hoelz, A.; "Crystal structure and mechanism of human lysine-specific demethylase-1."; Nat.Struct.Mol.Biol.; (2006) 13:626-632 PubMed:16799558.


author: Naoya Fujita

Japanese version:PDB:2H94