3k2o

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{{STRUCTURE_3k2o| PDB=3k2o | SCENE= }}
 
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===Structure of an oxygenase===
 
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{{ABSTRACT_PUBMED_20685276}}
 
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==Function==
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==Structure of an oxygenase==
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<StructureSection load='3k2o' size='340' side='right' caption='[[3k2o]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3k2o]] 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=3K2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K2O 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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JMJD6, KIAA0585, PTDSR ([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='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=3k2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k2o OCA], [http://pdbe.org/3k2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k2o RCSB], [http://www.ebi.ac.uk/pdbsum/3k2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k2o ProSAT]</span></td></tr>
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</table>
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== Function ==
[[http://www.uniprot.org/uniprot/JMJD6_HUMAN JMJD6_HUMAN]] Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as a RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses.<ref>PMID:17947579</ref> <ref>PMID:19574390</ref> <ref>PMID:21060799</ref> <ref>PMID:20684070</ref> <ref>PMID:20679243</ref>
[[http://www.uniprot.org/uniprot/JMJD6_HUMAN JMJD6_HUMAN]] Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as a RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses.<ref>PMID:17947579</ref> <ref>PMID:19574390</ref> <ref>PMID:21060799</ref> <ref>PMID:20684070</ref> <ref>PMID:20679243</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k2/3k2o_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3k2o ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl residues in arginine-serine-rich domains of RNA-splicing-related proteins. We report crystallographic studies on the catalytic domain of JMJD6 in complex with Ni(II) substituting for Fe(II). Together with mutational studies, the structural data suggest how JMJD6 binds its lysyl residues such that it can catalyse C-5 hydroxylation rather than N(varepsilon)-demethylation, as for analogous enzymes.
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==About this Structure==
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Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6.,Mantri M, Krojer T, Bagg EA, Webby CA, Butler DS, Kochan G, Kavanagh KL, Oppermann U, McDonough MA, Schofield CJ J Mol Biol. 2010 May 31. PMID:20685276<ref>PMID:20685276</ref>
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[[3k2o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K2O OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<ref group="xtra">PMID:020685276</ref><references group="xtra"/><references/>
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</div>
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[[Category: Homo sapiens]]
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<div class="pdbe-citations 3k2o" style="background-color:#fffaf0;"></div>
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[[Category: Arrowsmith, C H.]]
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== References ==
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[[Category: Bhatia, C.]]
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<references/>
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[[Category: Bountra, C.]]
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__TOC__
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[[Category: Bray, J E.]]
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</StructureSection>
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[[Category: Butler, D S.]]
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[[Category: Human]]
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[[Category: Chaikuad, A.]]
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[[Category: Arrowsmith, C H]]
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[[Category: Clifton, I J.]]
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[[Category: Bhatia, C]]
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[[Category: Delft, F von.]]
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[[Category: Bountra, C]]
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[[Category: Edwards, A M.]]
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[[Category: Bray, J E]]
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[[Category: Gileadi, O.]]
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[[Category: Butler, D S]]
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[[Category: Kavanagh, K L.]]
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[[Category: Chaikuad, A]]
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[[Category: Kochan, G.]]
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[[Category: Clifton, I J]]
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[[Category: Krojer, T.]]
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[[Category: Delft, F von]]
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[[Category: Mantri, M.]]
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[[Category: Edwards, A M]]
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[[Category: McDonough, M A.]]
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[[Category: Gileadi, O]]
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[[Category: Ng, S S.]]
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[[Category: Kavanagh, K L]]
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[[Category: Oppermann, U.]]
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[[Category: Kochan, G]]
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[[Category: Pike, A C.W.]]
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[[Category: Krojer, T]]
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[[Category: Schofield, C J.]]
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[[Category: Mantri, M]]
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[[Category: Webby, C J.]]
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[[Category: McDonough, M A]]
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[[Category: Weigelt, J.]]
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[[Category: Ng, S S]]
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[[Category: Oppermann, U]]
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[[Category: Pike, A C.W]]
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[[Category: Structural genomic]]
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[[Category: Schofield, C J]]
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[[Category: Webby, C J]]
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[[Category: Weigelt, J]]
[[Category: Chromatin regulator]]
[[Category: Chromatin regulator]]
[[Category: Developmental protein]]
[[Category: Developmental protein]]
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[[Category: Oxidoreductase]]
[[Category: Oxidoreductase]]
[[Category: Sgc]]
[[Category: Sgc]]
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[[Category: Structural genomics consortium]]
 
[[Category: Transcription]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
[[Category: Transcription regulation]]

Current revision

Structure of an oxygenase

3k2o, resolution 1.75Å

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