2z5u

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{{Seed}}
 
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[[Image:2z5u.png|left|200px]]
 
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==Crystal structure of Lysine-specific histone demethylase 1==
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The line below this paragraph, containing "STRUCTURE_2z5u", creates the "Structure Box" on the page.
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<StructureSection load='2z5u' size='340' side='right'caption='[[2z5u]], [[Resolution|resolution]] 2.25&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'>[[2z5u]] 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=2Z5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z5U 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]] 2.25&#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=FAJ:FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE+ADDUCT'>FAJ</scene></td></tr>
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{{STRUCTURE_2z5u| PDB=2z5u | 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=2z5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z5u OCA], [https://pdbe.org/2z5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z5u RCSB], [https://www.ebi.ac.uk/pdbsum/2z5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z5u 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/z5/2z5u_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=2z5u 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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Transcriptional activity and chromatin structure accessibility are correlated with the methylation of specific histone residues. Lysine-specific demethylase 1 (LSD1) is the first discovered histone demethylase, which demethylates Lys4 or Lys9 of histone H3, using FAD. Among the known monoamine oxidase inhibitors, tranylcypromine (Parnate) showed the most potent inhibitory effect on LSD1. Recently, the crystal structure of LSD1 and tranylcypromine was solved at 2.75 A, revealing a five-membered ring fused to the flavin of LSD1. In this study, we refined the crystal structure of the LSD1-tranylcypromine complex to 2.25 A. The five-membered ring model did not fit completely with the electron density, giving R(work)/R(free) values of 0.226/0.254. On the other hand, the N(5) adduct gave the lowest R(work)/R(free) values of 0.218/0.248, among the tested models. These results imply that the LSD1-tranylcypromine complex is not completely composed of the five-membered adduct, but partially contains an intermediate, such as the N(5) adduct.
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===Crystal structure of Lysine-specific histone demethylase 1===
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Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25 A.,Mimasu S, Sengoku T, Fukuzawa S, Umehara T, Yokoyama S Biochem Biophys Res Commun. 2008 Feb 1;366(1):15-22. Epub 2007 Nov 26. PMID:18039463<ref>PMID:18039463</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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<div class="pdbe-citations 2z5u" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18039463}}, adds the Publication Abstract to the page
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*[[Lysine-specific histone demethylase 3D structures|Lysine-specific histone demethylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18039463 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18039463}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2Z5U is a 1 chain structure of 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=2Z5U OCA].
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==Reference==
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<ref group="xtra">PMID:18039463</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Mimasu, S.]]
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[[Category: Large Structures]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Mimasu S]]
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[[Category: Sengoku, T.]]
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[[Category: Sengoku T]]
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[[Category: Yokoyama, S.]]
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[[Category: Yokoyama S]]
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[[Category: Alternative splicing]]
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[[Category: Chromatin]]
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[[Category: Chromatin regulator]]
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[[Category: Coiled coil]]
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[[Category: Crystal structure]]
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[[Category: Fad]]
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[[Category: Histone demethylase]]
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[[Category: Lsd1]]
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[[Category: Lysine-specific]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Nucleosome]]
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[[Category: Nucleus]]
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[[Category: Oxidoreductase]]
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[[Category: Phosphorylation]]
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[[Category: Repressor]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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[[Category: Transcription]]
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[[Category: Transcription regulation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:37:49 2009''
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Current revision

Crystal structure of Lysine-specific histone demethylase 1

PDB ID 2z5u

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