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| | ==Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA)== | | ==Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA)== |
| - | <StructureSection load='6ax3' size='340' side='right' caption='[[6ax3]], [[Resolution|resolution]] 2.25Å' scene=''> | + | <StructureSection load='6ax3' size='340' side='right'caption='[[6ax3]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ax3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AX3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AX3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ax3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AX3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KDM8, JMJD5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Histone_H3]-lysine-36_demethylase [Histone H3]-lysine-36 demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.27 1.14.11.27] </span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ax3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ax3 OCA], [https://pdbe.org/6ax3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ax3 RCSB], [https://www.ebi.ac.uk/pdbsum/6ax3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ax3 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ax3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ax3 OCA], [http://pdbe.org/6ax3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ax3 RCSB], [http://www.ebi.ac.uk/pdbsum/6ax3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ax3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KDM8_HUMAN 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. | + | [https://www.uniprot.org/uniprot/KDM8_HUMAN 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. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6ax3" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6ax3" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Dai, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Lee, S]] | + | [[Category: Dai S]] |
| - | [[Category: Liu, H]] | + | [[Category: Lee S]] |
| - | [[Category: Wang, Y]] | + | [[Category: Liu H]] |
| - | [[Category: Zhang, G]] | + | [[Category: Wang Y]] |
| - | [[Category: Demethylase]]
| + | [[Category: Zhang G]] |
| - | [[Category: Endopeptidase]]
| + | |
| - | [[Category: Exopeptidase]]
| + | |
| - | [[Category: Histone]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Jumonji]]
| + | |
| Structural highlights
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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. Specific Recognition of Arginine Methylated Histone Tails by JMJD5 and JMJD7. Sci Rep. 2018 Feb 19;8(1):3275. doi: 10.1038/s41598-018-21432-8. PMID:29459673 doi:http://dx.doi.org/10.1038/s41598-018-21432-8
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