2v1d

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[[Image:2v1d.png|left|200px]]
 
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{{STRUCTURE_2v1d| PDB=2v1d | SCENE= }}
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==Structural basis of LSD1-CoREST selectivity in histone H3 recognition==
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<StructureSection load='2v1d' size='340' side='right'caption='[[2v1d]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2v1d]] is a 3 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=2V1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V1D 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]] 3.1&#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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=2v1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v1d OCA], [https://pdbe.org/2v1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v1d RCSB], [https://www.ebi.ac.uk/pdbsum/2v1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v1d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/KDM1A_HUMAN KDM1A_HUMAN] Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development.<ref>PMID:12032298</ref> <ref>PMID:15620353</ref> <ref>PMID:16079795</ref> <ref>PMID:17805299</ref> <ref>PMID:20228790</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/v1/2v1d_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=2v1d 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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Histone demethylase LSD1 regulates transcription by demethylating Lys(4) of histone H3. The crystal structure of the enzyme in complex with CoREST and a substrate-like peptide inhibitor highlights an intricate network of interactions and a folded conformation of the bound peptide. The core of the peptide structure is formed by Arg(2), Gln(5), and Ser(10), which are engaged in specific intramolecular H-bonds. Several charged side chains on the surface of the substrate-binding pocket establish electrostatic interactions with the peptide. The three-dimensional structure predicts that methylated Lys(4) binds in a solvent inaccessible position in front of the flavin cofactor. This geometry is fully consistent with the demethylation reaction being catalyzed through a flavin-mediated oxidation of the substrate amino-methyl group. These features dictate the exquisite substrate specificity of LSD1 and provide a structural framework to explain the fine tuning of its catalytic activity and the active role of CoREST in substrate recognition.
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===STRUCTURAL BASIS OF LSD1-COREST SELECTIVITY IN HISTONE H3 RECOGNITION===
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Structural basis of LSD1-CoREST selectivity in histone H3 recognition.,Forneris F, Binda C, Adamo A, Battaglioli E, Mattevi A J Biol Chem. 2007 Jul 13;282(28):20070-4. Epub 2007 May 30. PMID:17537733<ref>PMID:17537733</ref>
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{{ABSTRACT_PUBMED_17537733}}
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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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==About this Structure==
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<div class="pdbe-citations 2v1d" style="background-color:#fffaf0;"></div>
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[[2v1d]] is a 3 chain structure of [[Lysine-specific histone demethylase 1]] 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=2V1D OCA].
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==See Also==
==See Also==
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*[[Lysine-specific histone demethylase 1|Lysine-specific histone demethylase 1]]
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*[[Lysine-specific histone demethylase|Lysine-specific histone demethylase]]
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*[[Lysine-specific histone demethylase 3D structures|Lysine-specific histone demethylase 3D structures]]
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==Reference==
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== References ==
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<ref group="xtra">PMID:017537733</ref><references group="xtra"/>
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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: Adamo, A.]]
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[[Category: Large Structures]]
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[[Category: Battaglioli, E.]]
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[[Category: Adamo A]]
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[[Category: Binda, C.]]
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[[Category: Battaglioli E]]
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[[Category: Forneris, F.]]
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[[Category: Binda C]]
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[[Category: Mattevi, A.]]
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[[Category: Forneris F]]
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[[Category: Chromatin regulator]]
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[[Category: Mattevi A]]
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[[Category: Chromatin remodelling]]
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[[Category: Flavin]]
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[[Category: Host-virus interaction]]
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[[Category: Nuclear protein]]
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[[Category: Oxidoreductase]]
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[[Category: Oxidoreductase repressor complex]]
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[[Category: Oxidoreductase-repressor complex]]
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[[Category: Phosphorylation]]
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[[Category: Repressor]]
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[[Category: Transcription regulation]]
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Current revision

Structural basis of LSD1-CoREST selectivity in histone H3 recognition

PDB ID 2v1d

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