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| | ==60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG)== | | ==60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG)== |
| - | <StructureSection load='4bu2' size='340' side='right' caption='[[4bu2]], [[Resolution|resolution]] 2.78Å' scene=''> | + | <StructureSection load='4bu2' size='340' side='right'caption='[[4bu2]], [[Resolution|resolution]] 2.78Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4bu2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BU2 OCA]. <br> | + | <table><tr><td colspan='2'>[[4bu2]] 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=4BU2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BU2 FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=4bu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bu2 OCA], [https://pdbe.org/4bu2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bu2 RCSB], [https://www.ebi.ac.uk/pdbsum/4bu2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bu2 ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xdv|2xdv]], [[4bxf|4bxf]], [[4ccj|4ccj]], [[4cck|4cck]], [[4ccm|4ccm]], [[4ccn|4ccn]], [[4cco|4cco]], [[4diq|4diq]]</td></tr> | + | </table> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
| + | == Function == |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4bu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bu2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bu2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bu2 PDBsum]</span></td></tr>
| + | [[https://www.uniprot.org/uniprot/RIOX2_HUMAN RIOX2_HUMAN]] Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Is involved in the demethylation of trimethylated 'Lys-9' on histone H3 (H3K9me3), leading to an increase in ribosomal RNA expression. Also catalyzes the hydroxylation of 60S ribosomal protein L27a on 'His-39'. May play an important role in cell growth and survival. May be involved in ribosome biogenesis, most likely during the assembly process of pre-ribosomal particles.<ref>PMID:12091391</ref> <ref>PMID:14695334</ref> <ref>PMID:15534111</ref> <ref>PMID:15819408</ref> <ref>PMID:15897898</ref> <ref>PMID:17317935</ref> <ref>PMID:19502796</ref> <ref>PMID:23103944</ref> |
| - | <table> | + | |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed == | + | |
| - | The finding that oxygenase-catalyzed protein hydroxylation regulates animal transcription raises questions as to whether the translation machinery and prokaryotic proteins are analogously modified. Escherichia coli ycfD is a growth-regulating 2-oxoglutarate oxygenase catalyzing arginyl hydroxylation of the ribosomal protein Rpl16. Human ycfD homologs, Myc-induced nuclear antigen (MINA53) and NO66, are also linked to growth and catalyze histidyl hydroxylation of Rpl27a and Rpl8, respectively. This work reveals new therapeutic possibilities via oxygenase inhibition and by targeting modified over unmodified ribosomes.
| + | |
| - | | + | |
| - | Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans.,Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TD, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, McCullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ Nat Chem Biol. 2012 Dec;8(12):960-2. doi: 10.1038/nchembio.1093. Epub 2012 Oct, 28. PMID:23103944<ref>PMID:23103944</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div> | + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Chowdhury, R.]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Clifton, I J.]] | + | [[Category: Large Structures]] |
| - | [[Category: Mcdonough, M A.]] | + | [[Category: Chowdhury R]] |
| - | [[Category: Ng, S S.]] | + | [[Category: Clifton IJ]] |
| - | [[Category: Oppermann, U.]] | + | [[Category: McDonough MA]] |
| - | [[Category: Pilka, E.]] | + | [[Category: Ng SS]] |
| - | [[Category: Schofield, C J.]] | + | [[Category: Oppermann U]] |
| - | [[Category: 2-oxoglutarate]] | + | [[Category: Pilka E]] |
| - | [[Category: Beta-hydroxylation]] | + | [[Category: Schofield CJ]] |
| - | [[Category: Dioxygenase]]
| + | |
| - | [[Category: Dsbh]]
| + | |
| - | [[Category: Iron-binding]]
| + | |
| - | [[Category: Jmjc domain]]
| + | |
| - | [[Category: Non-heme]]
| + | |
| - | [[Category: Nuclear protein]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Ribosome biogenesis]]
| + | |
| - | [[Category: Rpl27a]]
| + | |
| - | [[Category: Signaling]]
| + | |
| - | [[Category: Transcription and epigenetic regulation]]
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| Structural highlights
Function
[RIOX2_HUMAN] Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Is involved in the demethylation of trimethylated 'Lys-9' on histone H3 (H3K9me3), leading to an increase in ribosomal RNA expression. Also catalyzes the hydroxylation of 60S ribosomal protein L27a on 'His-39'. May play an important role in cell growth and survival. May be involved in ribosome biogenesis, most likely during the assembly process of pre-ribosomal particles.[1] [2] [3] [4] [5] [6] [7] [8]
References
- ↑ Tsuneoka M, Koda Y, Soejima M, Teye K, Kimura H. A novel myc target gene, mina53, that is involved in cell proliferation. J Biol Chem. 2002 Sep 20;277(38):35450-9. Epub 2002 Jun 28. PMID:12091391 doi:10.1074/jbc.M204458200
- ↑ Teye K, Tsuneoka M, Arima N, Koda Y, Nakamura Y, Ueta Y, Shirouzu K, Kimura H. Increased expression of a Myc target gene Mina53 in human colon cancer. Am J Pathol. 2004 Jan;164(1):205-16. PMID:14695334
- ↑ Tsuneoka M, Fujita H, Arima N, Teye K, Okamura T, Inutsuka H, Koda Y, Shirouzu K, Kimura H. Mina53 as a potential prognostic factor for esophageal squamous cell carcinoma. Clin Cancer Res. 2004 Nov 1;10(21):7347-56. PMID:15534111 doi:10/21/7347
- ↑ Eilbracht J, Kneissel S, Hofmann A, Schmidt-Zachmann MS. Protein NO52--a constitutive nucleolar component sharing high sequence homologies to protein NO66. Eur J Cell Biol. 2005 Mar;84(2-3):279-94. PMID:15819408
- ↑ Zhang Y, Lu Y, Yuan BZ, Castranova V, Shi X, Stauffer JL, Demers LM, Chen F. The Human mineral dust-induced gene, mdig, is a cell growth regulating gene associated with lung cancer. Oncogene. 2005 Jul 21;24(31):4873-82. PMID:15897898 doi:1208668
- ↑ Kuratomi K, Yano H, Tsuneoka M, Sakamoto K, Kusukawa J, Kojiro M. Immunohistochemical expression of Mina53 and Ki67 proteins in human primary gingival squamous cell carcinoma. Kurume Med J. 2006;53(3-4):71-8. PMID:17317935
- ↑ Lu Y, Chang Q, Zhang Y, Beezhold K, Rojanasakul Y, Zhao H, Castranova V, Shi X, Chen F. Lung cancer-associated JmjC domain protein mdig suppresses formation of tri-methyl lysine 9 of histone H3. Cell Cycle. 2009 Jul 1;8(13):2101-9. Epub 2009 Jul 5. PMID:19502796
- ↑ Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TD, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, McCullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat Chem Biol. 2012 Dec;8(12):960-2. doi: 10.1038/nchembio.1093. Epub 2012 Oct, 28. PMID:23103944 doi:10.1038/nchembio.1093
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