4gur: Difference between revisions

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-{{STRUCTURE_4gur|  PDB=4gur  |  SCENE=  }}
+==Crystal structure of LSD2-NPAC with H3 in space group P21==
-===Crystal structure of LSD2-NPAC with H3 in space group P21===
+<StructureSection load='4gur' size='340' side='right' caption='[[4gur]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
-{{ABSTRACT_PUBMED_23260659}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4gur]] is a 3 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=4GUR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GUR FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gu1|4gu1]], [[4gus|4gus]], [[4gut|4gut]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LSD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), GLYR1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gur OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gur RCSB], [http://www.ebi.ac.uk/pdbsum/4gur PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dynamic regulation of histone methylation represents a fundamental epigenetic mechanism underlying eukaryotic gene regulation, yet little is known about how the catalytic activities of histone demethylases are regulated. Here, we identify and characterize NPAC/GLYR1 as an LSD2/KDM1b-specific cofactor that stimulates H3K4me1 and H3K4me2 demethylation. We determine the crystal structures of LSD2 alone and LSD2 in complex with the NPAC linker region in the absence or presence of histone H3 peptide, at resolutions of 2.9, 2.0, and 2.25 A, respectively. These crystal structures and further biochemical characterization define a dodecapeptide of NPAC (residues 214-225) as the minimal functional unit for its cofactor activity and provide structural determinants and a molecular mechanism underlying the intrinsic cofactor activity of NPAC in stimulating LSD2-catalyzed H3K4 demethylation. Thus, these findings establish a model for how a cofactor directly regulates histone demethylation and will have a significant impact on our understanding of catalytic-activity-based epigenetic regulation.
-==Function==
+LSD2/KDM1B and Its Cofactor NPAC/GLYR1 Endow a Structural and Molecular Model for Regulation of H3K4 Demethylation.,Fang R, Chen F, Dong Z, Hu D, Barbera AJ, Clark EA, Fang J, Yang Y, Mei P, Rutenberg M, Li Z, Zhang Y, Xu Y, Yang H, Wang P, Simon MD, Zhou Q, Li J, Marynick MP, Li X, Lu H, Kaiser UB, Kingston RE, Xu Y, Shi YG Mol Cell. 2012 Dec 19. pii: S1097-2765(12)00976-8. doi:, 10.1016/j.molcel.2012.11.019. PMID:23260659<ref>PMID:23260659</ref>
-[[http://www.uniprot.org/uniprot/GLYR1_HUMAN GLYR1_HUMAN]] May have oxidoreductase activity. Regulates p38 MAP kinase activity by mediating stress activation of p38alpha/MAPK14 and specifically regulating MAPK14 signaling. Indirectly promotes phosphorylation of MAPK14 and activation of ATF2. The phosphorylation of MAPK14 requires upstream activity of MAP2K4 and MAP2K6. Recruited on chromatin, recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3).<ref>PMID:16352664</ref> <ref>PMID:20850016</ref>
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[4gur]] is a 3 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=4GUR OCA].
+</div>
-==Reference==
+==See Also==
-<ref group="xtra">PMID:023260659</ref><references group="xtra"/><references/>
+*[[Lysine-specific histone demethylase 1|Lysine-specific histone demethylase 1]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Chen, F.]]
+[[Category: Chen, F]]
-[[Category: Dong, Z.]]
+[[Category: Dong, Z]]
-[[Category: Fang, J.]]
+[[Category: Fang, J]]
-[[Category: Fang, R.]]
+[[Category: Fang, R]]
-[[Category: Li, Z.]]
+[[Category: Li, Z]]
-[[Category: Shi, Y.]]
+[[Category: Shi, Y]]
-[[Category: Wang, P.]]
+[[Category: Wang, P]]
-[[Category: Xu, Y.]]
+[[Category: Xu, Y]]
-[[Category: Yang, H.]]
+[[Category: Yang, H]]
-[[Category: Yang, Y.]]
+[[Category: Yang, Y]]
 [[Category: Histone demethylase]]
 [[Category: Oxidoreductase]]