2dw4

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:48, 13 March 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2dw4.png|left|200px]]
 
-
{{STRUCTURE_2dw4| PDB=2dw4 | SCENE= }}
+
==Crystal structure of human LSD1 at 2.3 A resolution==
-
 
+
<StructureSection load='2dw4' size='340' side='right'caption='[[2dw4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-
===Crystal structure of human LSD1 at 2.3 A resolution===
+
== Structural highlights ==
-
 
+
<table><tr><td colspan='2'>[[2dw4]] 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=2DW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DW4 FirstGlance]. <br>
-
{{ABSTRACT_PUBMED_18039463}}
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-
 
+
<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>
-
==About this Structure==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw4 OCA], [https://pdbe.org/2dw4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dw4 RCSB], [https://www.ebi.ac.uk/pdbsum/2dw4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw4 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dw4 TOPSAN]</span></td></tr>
-
[[2dw4]] is a 1 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=2DW4 OCA].
+
</table>
 +
== Function ==
 +
[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>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/2dw4_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=2dw4 ConSurf].
 +
<div style="clear:both"></div>
==See Also==
==See Also==
-
*[[Lysine-specific histone demethylase 1|Lysine-specific histone demethylase 1]]
+
*[[Lysine-specific histone demethylase 3D structures|Lysine-specific histone demethylase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:018039463</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
[[Category: Large Structures]]
-
[[Category: Sengoku, T.]]
+
[[Category: Sengoku T]]
-
[[Category: Yokoyama, S.]]
+
[[Category: Yokoyama S]]
-
[[Category: Amine oxidase]]
+
-
[[Category: Androgen]]
+
-
[[Category: Chromatin]]
+
-
[[Category: Corepressor]]
+
-
[[Category: Demethylase]]
+
-
[[Category: Fad]]
+
-
[[Category: Histone]]
+
-
[[Category: National project on protein structural and functional analyse]]
+
-
[[Category: Nppsfa]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Riken structural genomics/proteomics initiative]]
+
-
[[Category: Rsgi]]
+
-
[[Category: Structural genomic]]
+

Current revision

Crystal structure of human LSD1 at 2.3 A resolution

PDB ID 2dw4

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dw4"
Personal tools