3ld8

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[[Image:3ld8.png|left|200px]]
 
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==Structure of JMJD6 and Fab Fragments==
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The line below this paragraph, containing "STRUCTURE_3ld8", creates the "Structure Box" on the page.
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<StructureSection load='3ld8' size='340' side='right'caption='[[3ld8]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3ld8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Nothocricetulus_migratorius Nothocricetulus migratorius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LD8 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_3ld8| PDB=3ld8 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ld8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ld8 OCA], [https://pdbe.org/3ld8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ld8 RCSB], [https://www.ebi.ac.uk/pdbsum/3ld8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ld8 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://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/ld/3ld8_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3ld8 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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JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds alpha-ketoglutarate and iron and has been characterized as either a histone arginine demethylase or U2AF65 lysyl hydroxylase. Here, we describe the structures of JMJD6 with and without alpha-ketoglutarate, which revealed a novel substrate binding groove and two positively charged surfaces. The structures also contain a stack of aromatic residues located near the active center. The side chain of one residue within this stack assumed different conformations in the two structures. Interestingly, JMJD6 bound efficiently to single-stranded RNA, but not to single-stranded DNA, double-stranded RNA, or double-stranded DNA. These structural features and truncation analysis of JMJD6 suggest that JMJD6 may bind and modify single-stand RNA rather than the previously reported peptide substrates.
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===Structure of JMJD6 and Fab Fragments===
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Interaction of JMJD6 with single-stranded RNA.,Hong X, Zang J, White J, Wang C, Pan CH, Zhao R, Murphy RC, Dai S, Henson P, Kappler JW, Hagman J, Zhang G Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14568-72. Epub 2010 Aug 2. PMID:20679243<ref>PMID:20679243</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3ld8" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20679243 is the PubMed ID number.
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{{ABSTRACT_PUBMED_20679243}}
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==About this Structure==
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[[3ld8]] is a 3 chain structure of [[Monoclonal Antibody]] with sequence from [http://en.wikipedia.org/wiki/Cricetulus_migratorius Cricetulus migratorius] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LD8 OCA].
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==See Also==
==See Also==
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*[[Monoclonal Antibody|Monoclonal Antibody]]
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*[[Antibody 3D structures|Antibody 3D structures]]
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*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
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==Reference==
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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<ref group="xtra">PMID:020679243</ref><references group="xtra"/>
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== References ==
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[[Category: Cricetulus migratorius]]
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Hong, X.]]
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[[Category: Large Structures]]
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[[Category: Kappler, J W.]]
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[[Category: Nothocricetulus migratorius]]
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[[Category: Wang, C.]]
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[[Category: Hong X]]
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[[Category: White, J.]]
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[[Category: Kappler JW]]
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[[Category: Zang, J.]]
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[[Category: Wang C]]
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[[Category: Zhang, G.]]
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[[Category: White J]]
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[[Category: Fab fragment]]
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[[Category: Zang J]]
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[[Category: Immune system]]
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[[Category: Zhang G]]
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[[Category: Jmjd6]]
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Current revision

Structure of JMJD6 and Fab Fragments

PDB ID 3ld8

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