3k3n

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{{STRUCTURE_3k3n| PDB=3k3n | SCENE= }}
 
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===Crystal structure of the catalytic core domain of human PHF8===
 
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==Disease==
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==Crystal structure of the catalytic core domain of human PHF8==
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[[http://www.uniprot.org/uniprot/PHF8_HUMAN PHF8_HUMAN]] Defects in PHF8 are the cause of mental retardation syndromic X-linked Siderius type (MRXSSD) [MIM:[http://omim.org/entry/300263 300263]]. A disorder characterized by mild to borderline mental retardation with or without cleft lip/cleft palate.<ref>PMID:20548336</ref><ref>PMID:20346720</ref><ref>PMID:20421419</ref><ref>PMID:20208542</ref><ref>PMID:20622853</ref><ref>PMID:20622854</ref><ref>PMID:20101266</ref><ref>PMID:16199551</ref><ref>PMID:17661819</ref>
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<StructureSection load='3k3n' size='340' side='right'caption='[[3k3n]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3k3n]] 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=3K3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K3N FirstGlance]. <br>
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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]] 2.4&#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=FE2:FE+(II)+ION'>FE2</scene></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=3k3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k3n OCA], [https://pdbe.org/3k3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k3n RCSB], [https://www.ebi.ac.uk/pdbsum/3k3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k3n ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/PHF8_HUMAN PHF8_HUMAN] Defects in PHF8 are the cause of mental retardation syndromic X-linked Siderius type (MRXSSD) [MIM:[https://omim.org/entry/300263 300263]. A disorder characterized by mild to borderline mental retardation with or without cleft lip/cleft palate.<ref>PMID:20548336</ref> <ref>PMID:20346720</ref> <ref>PMID:20421419</ref> <ref>PMID:20208542</ref> <ref>PMID:20622853</ref> <ref>PMID:20622854</ref> <ref>PMID:20101266</ref> <ref>PMID:16199551</ref> <ref>PMID:17661819</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/PHF8_HUMAN PHF8_HUMAN] Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20' residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May also have weak activity toward dimethylated H3 'Lys-36' (H3K36Me2), however, the relevance of this result remains unsure in vivo. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2 when binding H3K4me3.<ref>PMID:20531378</ref> <ref>PMID:20548336</ref> <ref>PMID:19843542</ref> <ref>PMID:20346720</ref> <ref>PMID:20421419</ref> <ref>PMID:20208542</ref> <ref>PMID:20622853</ref> <ref>PMID:20622854</ref> <ref>PMID:20101266</ref> <ref>PMID:20023638</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/k3/3k3n_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=3k3n 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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Dynamic regulation of histone methylation/demethylation plays an important role during development. Mutations and truncations in human plant homeodomain (PHD) finger protein 8 (PHF8) are associated with X-linked mental retardation and facial anomalies, such as a long face, broad nasal tip, cleft lip/cleft palate and large hands, yet its molecular function and structural basis remain unclear. Here, we report the crystal structures of the catalytic core of PHF8 with or without alpha-ketoglutarate (alpha-KG) at high resolution. Biochemical and structural studies reveal that PHF8 is a novel histone demethylase specific for di- and mono-methylated histone H3 lysine 9 (H3K9me2/1), but not for H3K9me3. Our analyses also reveal how human PHF8 discriminates between methylation states and achieves sequence specificity for methylated H3K9. The in vitro demethylation assay also showed that the F279S mutant observed in clinical patients possesses no demethylation activity, suggesting that loss of enzymatic activity is crucial for pathogenesis of PHF8 patients. Taken together, these results will shed light on the molecular mechanism underlying PHF8-associated developmental and neurological diseases.
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==Function==
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Structural insights into a novel histone demethylase PHF8.,Yu L, Wang Y, Huang S, Wang J, Deng Z, Zhang Q, Wu W, Zhang X, Liu Z, Gong W, Chen Z Cell Res. 2010 Jan 26. PMID:20101266<ref>PMID:20101266</ref>
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[[http://www.uniprot.org/uniprot/PHF8_HUMAN PHF8_HUMAN]] Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20' residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Required for brain development, probably by regulating expression of neuron-specific genes. Only has activity toward H4K20Me1 when nucleosome is used as a substrate and when not histone octamer is used as substrate. May also have weak activity toward dimethylated H3 'Lys-36' (H3K36Me2), however, the relevance of this result remains unsure in vivo. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: has weak activity toward H3K9Me2 in absence of H3K4me3, while it has high activity toward H3K9me2 when binding H3K4me3.<ref>PMID:20531378</ref><ref>PMID:20548336</ref><ref>PMID:19843542</ref><ref>PMID:20346720</ref><ref>PMID:20421419</ref><ref>PMID:20208542</ref><ref>PMID:20622853</ref><ref>PMID:20622854</ref><ref>PMID:20101266</ref><ref>PMID:20023638</ref>
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[3k3n]] is a 1 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=3K3N OCA].
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</div>
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<div class="pdbe-citations 3k3n" style="background-color:#fffaf0;"></div>
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==Reference==
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== References ==
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<references group="xtra"/><references/>
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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: Chen, Z.]]
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[[Category: Large Structures]]
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[[Category: Deng, Z.]]
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[[Category: Chen Z]]
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[[Category: Gong, W.]]
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[[Category: Deng Z]]
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[[Category: Huang, S.]]
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[[Category: Gong W]]
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[[Category: Wang, J.]]
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[[Category: Huang S]]
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[[Category: Wang, Y.]]
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[[Category: Wang J]]
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[[Category: Wu, W.]]
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[[Category: Wang Y]]
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[[Category: Yu, L.]]
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[[Category: Wu W]]
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[[Category: Chromatin modification]]
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[[Category: Yu L]]
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[[Category: Histone demethylase]]
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[[Category: Mental retardation]]
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[[Category: Metal-binding]]
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[[Category: Methylated h3k9]]
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[[Category: Oxidoreductase]]
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[[Category: Phosphoprotein]]
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[[Category: Zinc-finger]]
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Current revision

Crystal structure of the catalytic core domain of human PHF8

PDB ID 3k3n

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