2nyr: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin==
-<StructureSection load='2nyr' size='340' side='right' caption='[[2nyr]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
+<StructureSection load='2nyr' size='340' side='right'caption='[[2nyr]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nyr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fzq 2fzq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NYR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nyr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fzq 2fzq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NYR FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SVR:8,8-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC+ACID'>SVR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.06&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SIRT5, SIR2L5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SVR:8,8-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC+ACID'>SVR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2nyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nyr RCSB], [http://www.ebi.ac.uk/pdbsum/2nyr PDBsum]</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=2nyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nyr OCA], [https://pdbe.org/2nyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nyr RCSB], [https://www.ebi.ac.uk/pdbsum/2nyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nyr ProSAT]</span></td></tr>
-<table>
+</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>
 == 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/ny/2nyr_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/2nyr_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2nyr ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2nyr" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Journal:JBSD:28|Journal:JBSD:28]]
+*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
 == References ==
 <references/>
@@ Line 33: / Line 37: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Allali-Hassani, A.]]
+[[Category: Large Structures]]
-[[Category: Antoshenko, T.]]
+[[Category: Allali-Hassani A]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Antoshenko T]]
-[[Category: Bochkarev, A.]]
+[[Category: Arrowsmith CH]]
-[[Category: Dong, A.]]
+[[Category: Bochkarev A]]
-[[Category: Edwards, A M.]]
+[[Category: Dong A]]
-[[Category: Min, J R.]]
+[[Category: Edwards AM]]
-[[Category: Plotnikov, A N.]]
+[[Category: Min JR]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Plotnikov AN]]
-[[Category: Sundstrom, M.]]
+[[Category: Sundstrom M]]
-[[Category: Weigelt, J.]]
+[[Category: Weigelt J]]
-[[Category: Histone deacetylase]]
-[[Category: Hydrolase]]
-[[Category: Sgc]]
-[[Category: Structural genomic]]
-[[Category: Structural genomics consortium]]