Structural Basis of LSD1-CoREST Selectivity in Histone H3 Recognition

Abstract

Histone demethylase LSD1 regulates transcription by demethylating Lys 4 of histone H3. The crystal structure of the enzyme in complex with CoREST and a substrate-like peptide inhibitor highlights an intricate network of interactions and a folded conformation of the bound peptide. The core of the peptide structure is formed by Arg 2 , Gln 5 , and Ser 10 , which are engaged in specific intramolecular H-bonds. Several charged side chains on the surface of the substrate-binding pocket establish electrostatic interactions with the peptide. The three-dimensional structure predicts that methylated Lys 4 binds in a solvent inaccessible position in front of the flavin cofactor. This geometry is fully consistent with the demethylation reaction being catalyzed through a flavin-mediated oxidation of the substrate amino-methyl group. These features dictate the exquisite substrate specificity of LSD1 and provide a structural framework to explain the fine tuning of its catalytic activity and the active role of CoREST in substrate recognition.Lysine methylation is among the most well characterized histone modifications, and its existence has been known since the early days of chromatin research (1, 2). This type of epigenetic mark provides a huge potential for functional responses in that it can occur in different forms (mono-, di-, and tri-methylation) and on different histone sites, each having a specific physiological meaning. Histone methylation has been long thought to be a low turnover epigenetic mark, but the recent discovery of histone demethylases (3, 4) has challenged this view by demonstrating that histone lysine methylation can be actively and dynamically regulated. Two classes of histone demethylases have been uncovered; the enzymes of the JmjC family use iron as cofactor, whereas lysine-specific demethylase 1 (LSD1) 4 employs FAD as the prosthetic group (5).LSD1 catalyzes the oxidative demethylation of mono-and dimethyl Lys 4 of histone H3, generating hydrogen peroxide and formaldehyde (3, 4). The enzyme is implicated as a key component of distinct co-activator and co-repressor complexes in a surprisingly wide range of cellular processes where it participates in the dynamic transition of transcriptional programs (6). Its catalytic activity is finely tuned by the epigenetic marks present on the H3 N-terminal tail (7) and by other protein partners, such as CoREST, that form a stable complex with the enzyme (8, 9). The three-dimensional structure of LSD1 in its native state (10, 11) and in complex with the LSD1-binding domain of CoREST (12) have revealed that the catalytic center is located in the core of the enzyme main body. A protruding tower domain consisting of two remarkably long helices forms the docking site for the co-repressor protein (Fig. 1A).Here, we describe the structural analysis of LSD1-CoREST bound to a 21-amino acid H3 peptide in which pLys 4 ("p" is for peptide) is mutated to Met. The structural analysis illuminates the molecular properties that enable LSD1 to function as a key transcriptional reg...

Exploring the binding diversity of intrinsically disordered proteins involved in one‐to‐many binding

“…6(E)]. 70 A substrate-like peptide was generated by a K5M mutation (marked in gray in Fig. 6) because this mutation led to 30-fold increase in binding affinity thereby helping to stabilize the complex.…”

Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans

“…Some of them can remove methyl groups from two different lysine residues and, therefore, are dual-specificity histone demethylases. The crystal structure of LSD1 has been solved [38,[40][41][42] and the molecular determination for the sequence and methylation-state specificity has been uncovered. Although the structure of JMJD2A has been solved in apo form or in complex with its substrates [24][25][26][27], which provides insights into the molecular npg mechanism of catalysis and substrate recognition, how substrate specificity is determined for all other members of the JmjC domain-containing histone lysine demethylases remains to be elucidated.…”

“…Consistently, the H3K4me2 demethylase LSD1 also has a shallow active site, even though it uses a different enzymatic mechanism, and its active site shares no sequence similarity to ceKDM7A and other JmjC domain-containing proteins. In the LSD1 complex with H3 peptide analog (K4 is replaced by Met) [38], the distance between Cα and the reactive N-5 of flavin is 7.69 Å ( Figure 6B and Supplementary information, Figure S7). On the contrary, H3K9me3 and H3K36me3 demethylase JMJD2A has a large active site.…”

Synthesis and evaluation of 3-amino/guanidine substituted phenyl oxazoles as a novel class of LSD1 inhibitors with anti-proliferative properties

“…Finally, on deprotection with trifluoroacetic acid, 3-guanidine phenyl oxazole derivatives 9 were obtained. 26 A number of N-substituted derivatives (10)(11)(12)(13)(14) were also prepared via N-acylation, N-sulfonation or N-alkylation of 6b (Scheme 2). All synthesized compounds were fully characterized by spectroscopic methods (NMR, IR, MS and HRMS).…”

“…Using the available X-ray diffraction crystal structure of LSD1 as a starting point, 14 we designed a series of small molecules as potential inhibitors taking the key pharmacophore features identified for the MAO, the polyamine/guanidine and methionine based peptide inhibitors, into account ( Fig. 1) 12,13,15-20 being linked through an oxazole moiety.…”