3kqi

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{{Seed}}
 
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[[Image:3kqi.png|left|200px]]
 
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==crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide==
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The line below this paragraph, containing "STRUCTURE_3kqi", creates the "Structure Box" on the page.
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<StructureSection load='3kqi' size='340' side='right'caption='[[3kqi]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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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'>[[3kqi]] is a 2 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=3KQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KQI 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]] 1.78&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_3kqi| PDB=3kqi | 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=3kqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kqi OCA], [https://pdbe.org/3kqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kqi RCSB], [https://www.ebi.ac.uk/pdbsum/3kqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kqi ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PHF2_HUMAN PHF2_HUMAN] Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.<ref>PMID:21532585</ref> <ref>PMID:20129925</ref> <ref>PMID:21167174</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/kq/3kqi_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=3kqi 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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Distinct lysine methylation marks on histones create dynamic signatures deciphered by the "effector" modules, although the underlying mechanisms remain unclear. We identified the plant homeodomain- and Jumonji C domain-containing protein PHF2 as a novel histone H3K9 demethylase. We show in biochemical and crystallographic analyses that PHF2 recognizes histone H3K4 trimethylation through its plant homeodomain finger and that this interaction is essential for PHF2 occupancy and H3K9 demethylation at rDNA promoters. Our study provides molecular insights into the mechanism by which distinct effector domains within a protein cooperatively modulate the "cross-talk" of histone modifications.
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===crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide===
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Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation.,Wen H, Li J, Song T, Lu M, Kan PY, Lee MG, Sha B, Shi X J Biol Chem. 2010 Mar 26;285(13):9322-6. Epub 2010 Feb 2. PMID:20129925<ref>PMID:20129925</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>
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The line below this paragraph, {{ABSTRACT_PUBMED_20129925}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3kqi" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20129925 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20129925}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3KQI is a 2 chains structure with sequences 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=3KQI OCA].
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==Reference==
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<ref group="xtra">PMID:20129925</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Lee, M.]]
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[[Category: Large Structures]]
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[[Category: Li, J Z.]]
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[[Category: Lee M]]
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[[Category: Lu, M.]]
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[[Category: Li JZ]]
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[[Category: Song, T.]]
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[[Category: Lu M]]
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[[Category: Wen, H.]]
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[[Category: Song T]]
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[[Category: Histone-binding]]
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[[Category: Wen H]]
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[[Category: Metal-binding]]
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[[Category: Nuclear protein]]
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[[Category: Phd finger]]
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[[Category: Zinc-finger]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 21 09:16:33 2010''
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Current revision

crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide

PDB ID 3kqi

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