Sandbox Reserved 1491

This Sandbox is Reserved from 06/12/2018, through 30/06/2019 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1480 through Sandbox Reserved 1543.

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2xml - KDM4C catalytic domain

2xml is a 2 chain structure. This domain belongs to the Human KDM4C protein.

KDM4C is a histone demethylase involved in the specific demethylation of trimethylated residues (Lys 9 and Lys 36 of histone 3). These marks are specific tags for genes expression modification. KDM4C plays a main role in the modification of cell cycle genes expression and thus involved in the growth of tumoral cells.

spinqualitylabelsall models Structure of 2xml - monomeric domain of KDM4C Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Function Genes expression is directly related to the condensation state of the chromatin. Indeed, chromatin can be in the form of heterochromatin (condensed form of DNA) or euchromatin (relaxed form of DNA) which correspond respectively to the transcriptionally silent and active forms of DNA. Chromatin is composed of DNA wrapped around histone octamers forming nucleosomes. The histone tails residues can be acetylated, methylated or demethylated by enzymes in order to modify chromatin state and therefore gene expression. Different types of proteins involved in this process exist, such as histone acetylase (HAT), histone methylase (HMT) or histone demethylase (HDM). Two families of histone-lysine demethylase (KDM) have been identified as follows : the flavin (FAD)-dependent lysine-specific demethylases and the Fe(II)-dependent Jumonji C (JmjC) family. JmjC is subfamily of histone demethylases which regroups several proteins containing a specific catalytic domain called Jmjc found in 2xml structure. KDM4 demethylases belong to the JmjC family and contains six members : KDM4A-F. Enzymatic reaction of demethylation of H3K9(me3) and H3K36(me3) by KDM4C KDM4C/JMJD2 is a protein which converts specifically trimethylated histone residues to the dimethylated form. Indeed, it catalyzes the demethylation of both Lysine 9 and Lysine 36 of histone 3 (respectively H3K9me3 and H3K36me3 by hydroxylation of the lysine methyl group. This reaction leads to a dissociation of the methyl group from the lysine histone tail. KDM4C employs 2-oxoglutarate (OG), Fe2+ and oxygen as cosubstrates to promote its enzymatic reaction, thus the dissociation of one methyl group. Structural highlights 2xml is a monomeric domain composed of 348 amino acids. It is made up of two chains A and B. They are asymmetric, i.e. their sequence identities are below 95%. This domain is connected by a β-hairpin to the rest of the protein. This domain of KDM4C can bind to 5 ligands: Zn2+, Ni2+, N-Oxalylglycine (or OGA), Cl- (interaction only with chain A) and 1,2-ethanediol (or EDO; only with chain A) : - OGA: two binding sites (chains A and B). - EDO: three binding sites, only in chain A. They are linked to 2xml by hydrogen bond. - Zn2+: two binding sites (chains A and B). It makes four coordination bonds : with three cysteines and one histidine. - Ni2+ : two binding sites (chains A and B). It makes five coordination bonds : two with OGA, two with two histidine and a last one with a glutamic acid. - Cl- : one binding site, only in chain A. 2xml presents, in each of the two chains, parallel β sheets around OGA, forming an hydrophobic pocket (mainly made of aromatic acid). OGA interacts with 2xml amino acids through hydrogen bonds and coordination bonds with Ni2+. The sequence of the domain has been particularly preserved around OGA (when the protein is folded). Thus, the 3D structure has been very preserved as well, indicating that the structure around OGA is essential. Epigenetics Specific enzymes are directly involved in the modification of genes expression without altering the nucleotide sequence. They can modify the chromatin structure by adding (writers), reading (readers) or removing (erasers) marks : acetyl, methyl, phosphoryl groups, ubiquitin... These epigeneticmarks can either make the gene sequence more or less accessible for transcription factors depending on their nature, histones and labelled amino acids. All combinations of the nature and the localization of the marks form the histone code. KDM4C is a histone demethylase. This newly discovered class of proteins plays a central role in the epigenetic modifications : it removes the methyl group (which is very stable) from the epigenetically modified amino acid. Its actions has directed consequences on gene expression. By removing the third methyl group from Lysine 9 of histone 3 (H3K9me3), KDM4C promotes the formation of euchromatin and therefore transcriptional activation. However, KDM4C indirectly condenses chromatin by removing the third methyl group from Lysine 36 of histone 3 (H3K36me3), leading to a repression of target genes expression. Disease Cancer is a disease characterized by an abnormally high level of cell proliferation, known as a tumor. This uncontrolled growth is the result of a modification of genetic information and its expression. Cancer cells have several characteristics, related to the activity of KDM4C: - Insensitivity to signals that normally regulate cell multiplication (especially antiproliferative signals). - Unlimited cell division - Ability to invade the body and other organs. The development of cancer begins with the modification of the sequence and expression of the genes involved in the cell cycle. The transformation from healthy cells to cancer cells is carried out in two stages: carcinogenesis and tumorigenesis. During carcinogenesis, cells accumulate genetic abnormalities, particularly in oncogenic sequences. Oncogenes are positive regulators of cell proliferation. After a mutation, they become hyperactive and cause an excessive cellular growth. Gatekeeper genes (genes that allow the passage from one stage of the cell cycle to the next) can also be mutated, leading to uncontrolled cell proliferation. During tumorigenesis, cancer becomes invasive: cancer cells invade other healthy organs. KDM4C is involved in carcinogenesis as an oncogene. Indeed, by catalyzing the demethylation of H3K9-me3 (lysine 9 from trimethylated histones 3) to H3K9-me2 (lysine 9 from dimethylated histones 3), this protein increases the expression of its target genes. Several KDM4C target genes are involved in cell growth. For example, they influence mitogenic signalling - which promotes mitosis and cell division -, cell cycle regulation and translation. In cancer cells, KDM4C expression is enhanced. Thus, the growth of tumor cells is greatly increased. In addition, KDM4C is involved in the correct segregation of chromosomes. Its high presence in tumor cells therefore ensures their viability. Finally, KDM4C also plays a role in the tumorigenesis of certain cancers, such as breast cancer, since it allows the proliferation of cancer cells, their migration and their invasive capacity in the triple-negative breast cancer. For all the implications of KDM4C in different cancers, it is one of the main targets of anti-cancer treatments.