6ax3 | pdb_00006ax3

Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA)

spinqualitylabelsall models 6ax3, resolution 2.25Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6ax3 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.25Å Ligands: 2MR, AKG, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function KDM8_HUMAN Histone demethylase required for G2/M phase cell cycle progression. Specifically demethylates dimethylated 'Lys-36' (H3K36me2) of histone H3, an epigenetic repressive mark, thereby acting as a transcription activator. Regulates expression of CCNA1 (cyclin-A1), leading to regulate cancer cell proliferation. Publication Abstract from PubMed We have reported that JMJD5 and JMJD7 (JMJD5/7) are responsible for the clipping of arginine methylated histone tails to generate "tailless nucleosomes", which could release the pausing RNA polymerase II (Pol II) into productive transcription elongation. JMJD5/7 function as endopeptidases that cleave histone tails specifically adjacent to methylated arginine residues and continue to degrade N-terminal residues of histones via their aminopeptidase activity. Here, we report structural and biochemical studies on JMJD5/7 to understand the basis of substrate recognition and catalysis mechanism by this JmjC subfamily. Recognition between these enzymes and histone substrates is specific, which is reflected by the binding data between enzymes and substrates. High structural similarity between JMJD5 and JMJD7 is reflected by the shared common substrates and high binding affinity. However, JMJD5 does not bind to arginine methylated histone tails with additional lysine acetylation while JMJD7 does not bind to arginine methylated histone tails with additional lysine methylation. Furthermore, the complex structures of JMJD5 and arginine derivatives revealed a Tudor domain-like binding pocket to accommodate the methylated sidechain of arginine, but not lysine. There also exists a glutamine close to the catalytic center, which may suggest a unique imidic acid mediated catalytic mechanism for proteolysis by JMJD5/7. Specific Recognition of Arginine Methylated Histone Tails by JMJD5 and JMJD7.,Liu H, Wang C, Lee S, Ning F, Wang Y, Zhang Q, Chen Z, Zang J, Nix J, Dai S, Marrack P, Hagman J, Kappler J, Zhang G Sci Rep. 2018 Feb 19;8(1):3275. doi: 10.1038/s41598-018-21432-8. PMID:29459673 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Jumonji domain-containing protein 3D structures

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