6f4t
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)== | |
| + | <StructureSection load='6f4t' size='340' side='right' caption='[[6f4t]], [[Resolution|resolution]] 1.22Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6f4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F4T FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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> | ||
| + | <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> | ||
| + | <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]], [[6f4r|6f4r]], [[6f4s|6f4s]]</td></tr> | ||
| + | <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> | ||
| + | <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=6f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4t OCA], [http://pdbe.org/6f4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f4t RCSB], [http://www.ebi.ac.uk/pdbsum/6f4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4t ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == 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. [[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> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| - | + | 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> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 6f4t" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: 50S ribosomal protein L16 3-hydroxylase]] | ||
| + | [[Category: Chowdhury, R]] | ||
| + | [[Category: Islam, M S]] | ||
| + | [[Category: Schofield, C J]] | ||
| + | [[Category: 2-oxoglutarate]] | ||
| + | [[Category: 40s ribosomal protein s6]] | ||
| + | [[Category: Arginine hydroxylation]] | ||
| + | [[Category: Arginyl c-3 hydroxylase]] | ||
| + | [[Category: Beta-hydroxylation]] | ||
| + | [[Category: Cancer]] | ||
| + | [[Category: Cell structure]] | ||
| + | [[Category: Cytoplasm]] | ||
| + | [[Category: Development]] | ||
| + | [[Category: Dioxygenase]] | ||
| + | [[Category: Dna-binding]] | ||
| + | [[Category: Dsbh]] | ||
| + | [[Category: Epigenetic regulation]] | ||
| + | [[Category: Facial triad]] | ||
| + | [[Category: Hydroxylation]] | ||
| + | [[Category: Hypoxia]] | ||
| + | [[Category: Iron]] | ||
| + | [[Category: Jmjc]] | ||
| + | [[Category: Jmjc demethylase]] | ||
| + | [[Category: Jmjc domain]] | ||
| + | [[Category: Jmjc domain-containing protein 5]] | ||
| + | [[Category: Jmjc hydroxylase]] | ||
| + | [[Category: Jmjd5]] | ||
| + | [[Category: Kdm]] | ||
| + | [[Category: Kdm8]] | ||
| + | [[Category: Lysine-specific demethylase 8]] | ||
| + | [[Category: Metal-binding]] | ||
| + | [[Category: Non-heme]] | ||
| + | [[Category: Oxidoreductase]] | ||
| + | [[Category: Oxygenase]] | ||
| + | [[Category: Phosphorylation]] | ||
| + | [[Category: Polymorphism]] | ||
| + | [[Category: Post-translational modification]] | ||
| + | [[Category: Ptm]] | ||
| + | [[Category: Rcc1 domain-containing protein 1]] | ||
| + | [[Category: Rccd1]] | ||
| + | [[Category: Regulator of chromosome condensation]] | ||
| + | [[Category: Ribosome biogenesis]] | ||
| + | [[Category: Rps6]] | ||
| + | [[Category: Signaling]] | ||
| + | [[Category: Transcription]] | ||
| + | [[Category: Transcription activator/inhibitor]] | ||
| + | [[Category: Translation]] | ||
Revision as of 06:02, 4 April 2018
Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)
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Categories: 50S ribosomal protein L16 3-hydroxylase | Chowdhury, R | Islam, M S | Schofield, C J | 2-oxoglutarate | 40s ribosomal protein s6 | Arginine hydroxylation | Arginyl c-3 hydroxylase | Beta-hydroxylation | Cancer | Cell structure | Cytoplasm | Development | Dioxygenase | Dna-binding | Dsbh | Epigenetic regulation | Facial triad | Hydroxylation | Hypoxia | Iron | Jmjc | Jmjc demethylase | Jmjc domain | Jmjc domain-containing protein 5 | Jmjc hydroxylase | Jmjd5 | Kdm | Kdm8 | Lysine-specific demethylase 8 | Metal-binding | Non-heme | Oxidoreductase | Oxygenase | Phosphorylation | Polymorphism | Post-translational modification | Ptm | Rcc1 domain-containing protein 1 | Rccd1 | Regulator of chromosome condensation | Ribosome biogenesis | Rps6 | Signaling | Transcription | Transcription activator/inhibitor | Translation
