4bu2: Difference between revisions

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<StructureSection load='4bu2' size='340' side='right'caption='[[4bu2]], [[Resolution|resolution]] 2.78&Aring;' scene=''>
<StructureSection load='4bu2' size='340' side='right'caption='[[4bu2]], [[Resolution|resolution]] 2.78&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4bu2]] 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=4BU2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4BU2 FirstGlance]. <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 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=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
</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 id='NonStdRes'><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 id='related'><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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4bu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bu2 OCA], [http://pdbe.org/4bu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bu2 RCSB], [http://www.ebi.ac.uk/pdbsum/4bu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bu2 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/MINA_HUMAN MINA_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:15897898</ref> <ref>PMID:14695334</ref> <ref>PMID:15534111</ref> <ref>PMID:15819408</ref> <ref>PMID:17317935</ref> <ref>PMID:19502796</ref> <ref>PMID:23103944</ref> 
[[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components and in the hydroxylation of transcription factors and splicing factor proteins. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA and ribosomal proteins have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone Nepsilon-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases.
 
Ribosomal oxygenases are structurally conserved from prokaryotes to humans.,Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JR, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ Nature. 2014 May 11. doi: 10.1038/nature13263. PMID:24814345<ref>PMID:24814345</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4bu2" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chowdhury, R]]
[[Category: Chowdhury R]]
[[Category: Clifton, I J]]
[[Category: Clifton IJ]]
[[Category: McDonough, M A]]
[[Category: McDonough MA]]
[[Category: Ng, S S]]
[[Category: Ng SS]]
[[Category: Oppermann, U]]
[[Category: Oppermann U]]
[[Category: Pilka, E]]
[[Category: Pilka E]]
[[Category: Schofield, C J]]
[[Category: Schofield CJ]]
[[Category: 2-oxoglutarate]]
[[Category: Beta-hydroxylation]]
[[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]]

Latest revision as of 20:08, 7 September 2022

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)

Structural highlights

4bu2 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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

4bu2, resolution 2.78Å

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