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6f4r

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'''Unreleased structure'''
 
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The entry 6f4r is ON HOLD until Paper Publication
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==Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3)==
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<StructureSection load='6f4r' size='340' side='right'caption='[[6f4r]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[6f4r]] is a 2 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=6F4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F4R FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6f4m|6f4m]], [[6f4n|6f4n]], [[6f4o|6f4o]], [[6f4p|6f4p]], [[6f4q|6f4q]], [[6f4s|6f4s]], [[6f4t|6f4t]]</td></tr>
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<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>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/50S_ribosomal_protein_L16_3-hydroxylase 50S ribosomal protein L16 3-hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.47 1.14.11.47] </span></td></tr>
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<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=6f4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4r OCA], [http://pdbe.org/6f4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f4r RCSB], [http://www.ebi.ac.uk/pdbsum/6f4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4r ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[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. [[http://www.uniprot.org/uniprot/RCCD1_HUMAN RCCD1_HUMAN]] Acts as a coregulator of KDM8 to promote histone demethylase activity on di- and trimethylated 'Lys-36' (H3K36me2/me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with KDM8 (PubMed:24981860). Possibly together with KDM8, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha-tubulin deacetylation and cytoskeletal microtubule stability and thereby promoting cell migration and TGF-beta-induced epithelial to mesenchymal transition (EMT), potentially through the inhibition of KDM8 (PubMed:28455245).<ref>PMID:24981860</ref> <ref>PMID:28455245</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Oxygenase-catalysed post-translational modifications of basic protein residues, including lysyl hydroxylations and N(epsilon)-methyl lysyl demethylations, have important cellular roles. Jumonji-C (JmjC) domain-containing protein 5 (JMJD5), which genetic studies reveal is essential in animal development, is reported as a histone N(epsilon)-methyl lysine demethylase (KDM). Here we report how extensive screening with peptides based on JMJD5 interacting proteins led to the finding that JMJD5 catalyses stereoselective C-3 hydroxylation of arginine residues in sequences from human regulator of chromosome condensation domain-containing protein 1 (RCCD1) and ribosomal protein S6 (RPS6). High-resolution crystallographic analyses reveal overall fold, active site and substrate binding/product release features supporting the assignment of JMJD5 as an arginine hydroxylase rather than a KDM. The results will be useful in the development of selective oxygenase inhibitors for the treatment of cancer and genetic diseases.
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Authors:
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JMJD5 is a human arginyl C-3 hydroxylase.,Wilkins SE, Islam S, Gannon JM, Markolovic S, Hopkinson RJ, Ge W, Schofield CJ, Chowdhury R Nat Commun. 2018 Mar 21;9(1):1180. doi: 10.1038/s41467-018-03410-w. PMID:29563586<ref>PMID:29563586</ref>
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Description:
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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<div class="pdbe-citations 6f4r" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Jumonji domain-containing protein|Jumonji domain-containing protein]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: 50S ribosomal protein L16 3-hydroxylase]]
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[[Category: Human]]
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[[Category: Large Structures]]
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[[Category: Chowdhury, R]]
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[[Category: Islam, M S]]
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[[Category: Schofield, C J]]
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[[Category: 2-oxoglutarate]]
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[[Category: 40s ribosomal protein s6]]
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[[Category: Arginine hydroxylation]]
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[[Category: Arginyl c-3 hydroxylase]]
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[[Category: Beta-hydroxylation]]
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[[Category: Cancer]]
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[[Category: Cell structure]]
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[[Category: Cytoplasm]]
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[[Category: Development]]
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[[Category: Dioxygenase]]
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[[Category: Dna-binding]]
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[[Category: Dsbh]]
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[[Category: Epigenetic regulation]]
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[[Category: Facial triad]]
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[[Category: Hydroxylation]]
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[[Category: Hypoxia]]
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[[Category: Iron]]
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[[Category: Jmjc]]
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[[Category: Jmjc demethylase]]
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[[Category: Jmjc domain]]
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[[Category: Jmjc domain-containing protein 5]]
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[[Category: Jmjc hydroxylase]]
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[[Category: Jmjd5]]
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[[Category: Kdm]]
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[[Category: Kdm8]]
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[[Category: Lysine-specific demethylase 8]]
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[[Category: Metal-binding]]
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[[Category: Non-heme]]
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[[Category: Oxidoreductase]]
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[[Category: Oxygenase]]
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[[Category: Phosphorylation]]
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[[Category: Polymorphism]]
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[[Category: Post-translational modification]]
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[[Category: Ptm]]
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[[Category: Rcc1 domain-containing protein 1]]
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[[Category: Rccd1]]
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[[Category: Regulator of chromosome condensation]]
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[[Category: Ribosome biogenesis]]
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[[Category: Rps6]]
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[[Category: Signaling]]
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[[Category: Transcription]]
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[[Category: Transcription activator/inhibitor]]
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[[Category: Translation]]

Current revision

Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3)

PDB ID 6f4r

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