3rig: Difference between revisions

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-[[Image:3rig.png|left|200px]]
-<!--
+==Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase==
-The line below this paragraph, containing "STRUCTURE_3rig", creates the "Structure Box" on the page.
+<StructureSection load='3rig' size='340' side='right'caption='[[3rig]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3rig]] is a 4 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=3RIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RIG FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=TLY:(2S)-2-AZANYL-6-(ETHANETHIOYLAMINO)HEXANOIC+ACID'>TLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3rig|  PDB=3rig  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rig OCA], [https://pdbe.org/3rig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rig RCSB], [https://www.ebi.ac.uk/pdbsum/3rig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rig ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SIR5_HUMAN SIR5_HUMAN] NAD-dependent lysine demalonylase and desuccinylase that specifically removes malonyl and succinyl groups on target proteins. Activates CPS1 and contributes to the regulation of blood ammonia levels during prolonged fasting: acts by mediating desuccinylation of CPS1, thereby increasing CPS1 activity in response to elevated NAD levels during fasting. Activates SOD1 by mediating its desuccinylation, leading to reduced reactive oxygen species. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo. Can deacetylate cytochrome c (CYCS) and a number of other proteins in vitro.<ref>PMID:18680753</ref> <ref>PMID:21908771</ref> <ref>PMID:24140062</ref> <ref>PMID:22076378</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Silent information regulator 2 (Sir2) proteins (sirtuins) are nicotinamide adenine dinucleotide-dependent deacetylases that regulate important biological processes. Mammals have seven sirtuins, Sirt1 to Sirt7. Four of them (Sirt4 to Sirt7) have no detectable or very weak deacetylase activity. We found that Sirt5 is an efficient protein lysine desuccinylase and demalonylase in vitro. The preference for succinyl and malonyl groups was explained by the presence of an arginine residue (Arg(105)) and tyrosine residue (Tyr(102)) in the acyl pocket of Sirt5. Several mammalian proteins were identified with mass spectrometry to have succinyl or malonyl lysine modifications. Deletion of Sirt5 in mice appeared to increase the level of succinylation on carbamoyl phosphate synthase 1, which is a known target of Sirt5. Thus, protein lysine succinylation may represent a posttranslational modification that can be reversed by Sirt5 in vivo.
-===Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase===
+Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase.,Du J, Zhou Y, Su X, Yu JJ, Khan S, Jiang H, Kim J, Woo J, Kim JH, Choi BH, He B, Chen W, Zhang S, Cerione RA, Auwerx J, Hao Q, Lin H Science. 2011 Nov 11;334(6057):806-9. PMID:22076378<ref>PMID:22076378</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3rig" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22076378}}, adds the Publication Abstract to the page
+*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22076378 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22076378}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3rig]] is a 4 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=3RIG OCA].
-==Reference==
-<ref group="xtra">PMID:022076378</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Zhou, Y.]]
+[[Category: Large Structures]]
-[[Category: Hydrolase]]
+[[Category: Zhou Y]]
-[[Category: Mitochondria]]
-[[Category: Protein lysine demalonylase/desuccinylase]]
-[[Category: Rossmann fold]]
-[[Category: Zn-binding domain]]