5bwn: Difference between revisions

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 ==Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine==
-<StructureSection load='5bwn' size='340' side='right' caption='[[5bwn]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
+<StructureSection load='5bwn' size='340' side='right'caption='[[5bwn]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5bwn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BWN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5bwn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BWN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BWN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 1.942&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MYK:N~6~-TETRADECANOYL-L-LYSINE'>MYK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MYK:N~6~-TETRADECANOYL-L-LYSINE'>MYK</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">[[5bwl|5bwl]], [[5bwo|5bwo]], [[5bwp|5bwp]], [[5bwq|5bwq]]</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=5bwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwn OCA], [https://pdbe.org/5bwn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bwn RCSB], [https://www.ebi.ac.uk/pdbsum/5bwn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwn ProSAT]</span></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=5bwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bwn OCA], [http://pdbe.org/5bwn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bwn RCSB], [http://www.ebi.ac.uk/pdbsum/5bwn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bwn ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SIR3_HUMAN SIR3_HUMAN]] NAD-dependent protein deacetylase. Activates mitochondrial target proteins, including ACSS1, IDH2 and GDH by deacetylating key lysine residues. Contributes to the regulation of the cellular energy metabolism. Important for regulating tissue-specific ATP levels.<ref>PMID:16788062</ref> <ref>PMID:18680753</ref> <ref>PMID:18794531</ref> <ref>PMID:19535340</ref>
+[https://www.uniprot.org/uniprot/H3C_HUMAN H3C_HUMAN] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.<ref>PMID:21274551</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+SIRT1-7 play important roles in many biological processes and age-related diseases. In addition to a NAD(+) -dependent deacetylase activity, they can catalyze several other reactions, including the hydrolysis of long-chain fatty acyl lysine. To study the binding modes of sirtuins to long-chain acyl lysines, we solved the crystal structures of SIRT3 bound to either a H3K9-myristoylated- or a H3K9-palmitoylated peptide. Interaction of SIRT3 with the palmitoyl group led to unfolding of the alpha3-helix. The myristoyl and palmitoyl groups bind to the C-pocket and an allosteric site near the alpha3-helix, respectively. We found that the residues preceding the alpha3-helix determine the size of the C-pocket. The flexibility of the alpha2-alpha3 loop and the plasticity of the alpha3-helix affect the interaction with long-chain acyl lysine.
+Crystal structures of SIRT3 reveal that the alpha2-alpha3 loop and alpha3-helix affect the interaction with long-chain acyl lysine.,Gai W, Li H, Jiang H, Long Y, Liu D FEBS Lett. 2016 Sep;590(17):3019-28. doi: 10.1002/1873-3468.12345. Epub 2016 Aug , 24. PMID:27501476<ref>PMID:27501476</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5bwn" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Gai, W]]
+[[Category: Homo sapiens]]
-[[Category: Liu, D]]
+[[Category: Large Structures]]
-[[Category: Hydrolase]]
+[[Category: Synthetic construct]]
-[[Category: Peptide-hydrolase complex]]
+[[Category: Gai W]]
+[[Category: Liu D]]