2qpw: Difference between revisions

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 ==Methyltransferase domain of human PR domain-containing protein 2==
-<StructureSection load='2qpw' size='340' side='right' caption='[[2qpw]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
+<StructureSection load='2qpw' size='340' side='right'caption='[[2qpw]], [[Resolution|resolution]] 1.79&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qpw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QPW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qpw]] 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=2QPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QPW FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PRDM2, RIZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.79&#8491;</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=2qpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qpw OCA], [http://pdbe.org/2qpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qpw RCSB], [http://www.ebi.ac.uk/pdbsum/2qpw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qpw ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qpw OCA], [https://pdbe.org/2qpw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qpw RCSB], [https://www.ebi.ac.uk/pdbsum/2qpw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qpw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PRDM2_HUMAN PRDM2_HUMAN]] S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene.<ref>PMID:14633678</ref>
+[https://www.uniprot.org/uniprot/PRDM2_HUMAN PRDM2_HUMAN] S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene.<ref>PMID:14633678</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=2qpw ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-SET domain methyltransferases deposit methyl marks on specific histone tail lysine residues and play a major role in epigenetic regulation of gene transcription. We solved the structures of the catalytic domains of GLP, G9a, Suv39H2 and PRDM2, four of the eight known human H3K9 methyltransferases in their apo conformation or in complex with the methyl donating cofactor, and peptide substrates. We analyzed the structural determinants for methylation state specificity, and designed a G9a mutant able to tri-methylate H3K9. We show that the I-SET domain acts as a rigid docking platform, while induced-fit of the Post-SET domain is necessary to achieve a catalytically competent conformation. We also propose a model where long-range electrostatics bring enzyme and histone substrate together, while the presence of an arginine upstream of the target lysine is critical for binding and specificity. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.
-Structural biology of human H3K9 methyltransferases.,Wu H, Min J, Lunin VV, Antoshenko T, Dombrovski L, Zeng H, Allali-Hassani A, Campagna-Slater V, Vedadi M, Arrowsmith CH, Plotnikov AN, Schapira M PLoS One. 2010 Jan 11;5(1):e8570. PMID:20084102<ref>PMID:20084102</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2qpw" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Antoshenko, T]]
+[[Category: Large Structures]]
-[[Category: Arrowsmith, C H]]
+[[Category: Antoshenko T]]
-[[Category: Bochkarev, A]]
+[[Category: Arrowsmith CH]]
-[[Category: Dombrovski, L]]
+[[Category: Bochkarev A]]
-[[Category: Edwards, A M]]
+[[Category: Dombrovski L]]
-[[Category: Loppnau, P]]
+[[Category: Edwards AM]]
-[[Category: Lunin, V V]]
+[[Category: Loppnau P]]
-[[Category: Min, J]]
+[[Category: Lunin VV]]
-[[Category: Plotnikov, A N]]
+[[Category: Min J]]
-[[Category: Structural genomic]]
+[[Category: Plotnikov AN]]
-[[Category: Sundstrom, M]]
+[[Category: Sundstrom M]]
-[[Category: Weigelt, J]]
+[[Category: Weigelt J]]
-[[Category: Wu, H]]
+[[Category: Wu H]]
-[[Category: Activator]]
-[[Category: Alternative initiation]]
-[[Category: Alternative splicing]]
-[[Category: Dna-binding]]
-[[Category: Metal-binding]]
-[[Category: Methyltransferase]]
-[[Category: Nucleus]]
-[[Category: Phosphorylation]]
-[[Category: Sgc]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Zinc]]
-[[Category: Zinc-finger]]