3ldb

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==Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.==
==Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.==
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<StructureSection load='3ldb' size='340' side='right' caption='[[3ldb]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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<StructureSection load='3ldb' size='340' side='right'caption='[[3ldb]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ldb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Armenian_hamster Armenian hamster] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LDB FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ldb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Cricetulus_migratorius Cricetulus migratorius] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LDB 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=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <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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</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ld8|3ld8]]</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=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <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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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JMJD6, JMJD6 (1-403), 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'>[https://proteopedia.org/fgij/fg.htm?mol=3ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ldb OCA], [https://pdbe.org/3ldb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ldb RCSB], [https://www.ebi.ac.uk/pdbsum/3ldb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ldb ProSAT]</span></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=3ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ldb OCA], [http://pdbe.org/3ldb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ldb RCSB], [http://www.ebi.ac.uk/pdbsum/3ldb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ldb ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[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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[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>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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==See Also==
==See Also==
*[[Antibody 3D structures|Antibody 3D structures]]
*[[Antibody 3D structures|Antibody 3D structures]]
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*[[Jumonji domain-containing protein|Jumonji domain-containing protein]]
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*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Armenian hamster]]
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[[Category: Cricetulus migratorius]]
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[[Category: Human]]
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[[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: Hong X]]
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[[Category: Wang, C]]
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[[Category: Kappler JW]]
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[[Category: White, J]]
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[[Category: Wang C]]
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[[Category: Zang, J]]
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[[Category: White J]]
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[[Category: Zhang, G]]
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[[Category: Zang J]]
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[[Category: Alpha-ketoglutarate]]
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[[Category: Zhang G]]
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[[Category: Fab fragment]]
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[[Category: Immune system]]
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[[Category: Jmj6d]]
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Revision as of 08:35, 6 September 2023

Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.

PDB ID 3ldb

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