6f4o: Difference between revisions

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-'''Unreleased structure'''
-The entry 6f4o is ON HOLD  until Paper Publication
+==Human JMJD5 in complex with Mn(II) and Succinate.==
+<StructureSection load='6f4o' size='340' side='right' caption='[[6f4o]], [[Resolution|resolution]] 1.28&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6f4o]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F4O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F4O FirstGlance]. <br>
+</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=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6f4m|6f4m]], [[6f4n|6f4n]], [[6f4p|6f4p]], [[6f4q|6f4q]], [[6f4r|6f4r]], [[6f4s|6f4s]], [[6f4t|6f4t]]</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=6f4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4o OCA], [http://pdbe.org/6f4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f4o RCSB], [http://www.ebi.ac.uk/pdbsum/6f4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4o 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.
+<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.
-Authors: CHOWDHURY, R., Islam, M.S., SCHOFIELD, C.J.
+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>
-Description: JmjC Succinate (OPT4_D11)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6f4o" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: 50S ribosomal protein L16 3-hydroxylase]]
 [[Category: Chowdhury, R]]
-[[Category: Schofield, C.J]]
+[[Category: Islam, M S]]
-[[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]]