3d81: Difference between revisions

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-{{Seed}}
-[[Image:3d81.jpg|left|200px]]
-<!--
+==Sir2-S-alkylamidate complex crystal structure==
-The line below this paragraph, containing "STRUCTURE_3d81", creates the "Structure Box" on the page.
+<StructureSection load='3d81' size='340' side='right'caption='[[3d81]], [[Resolution|resolution]] 2.50&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'>[[3d81]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D81 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FZN:(2S)-2-AMINO-6-{[(1Z)-1-{[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]SULFANYL}ETHYLIDENE]AMINO}HEXANOIC+ACID'>FZN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3d81|  PDB=3d81  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d81 OCA], [https://pdbe.org/3d81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d81 RCSB], [https://www.ebi.ac.uk/pdbsum/3d81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d81 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NPD_THEMA NPD_THEMA] NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form. Has also depropionylation activity in vitro. Also able to ADP-ribosylate peptide substrates with Arg or Lys in the +2 position. The role of this function in vivo is not clear.<ref>PMID:17684016</ref> <ref>PMID:16905097</ref> <ref>PMID:19801667</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/d8/3d81_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=3d81 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Sirtuin enzymes comprise a unique class of NAD(+)-dependent protein deacetylases. Although structures of many sirtuin complexes have been determined, structural resolution of intermediate chemical steps are needed to understand the deacetylation mechanism. We report crystal structures of the bacterial sirtuin, Sir2Tm, in complex with an S-alkylamidate intermediate, analogous to the naturally occurring O-alkylamidate intermediate, and a Sir2Tm ternary complex containing a dissociated NAD(+) analog and acetylated peptide. The structures and biochemical studies reveal critical roles for the invariant active site histidine in positioning the reaction intermediate, and for a conserved phenylalanine residue in shielding reaction intermediates from base exchange with nicotinamide. The new structural and biochemical studies provide key mechanistic insight into intermediate steps of the Sir2 deacetylation reaction.
-===Sir2-S-alkylamidate complex crystal structure===
+Structural insights into intermediate steps in the Sir2 deacetylation reaction.,Hawse WF, Hoff KG, Fatkins DG, Daines A, Zubkova OV, Schramm VL, Zheng W, Wolberger C Structure. 2008 Sep 10;16(9):1368-77. PMID:18786399<ref>PMID:18786399</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18786399}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3d81" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18786399 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18786399}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-D81 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D81 OCA].
-==Reference==
-Structural insights into intermediate steps in the Sir2 deacetylation reaction., Hawse WF, Hoff KG, Fatkins DG, Daines A, Zubkova OV, Schramm VL, Zheng W, Wolberger C, Structure. 2008 Sep 10;16(9):1368-77. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18786399 18786399]
-[[Category: Protein complex]]
 [[Category: Thermotoga maritima]]
-[[Category: Daines, A.]]
+[[Category: Daines A]]
-[[Category: Fatkins, D.]]
+[[Category: Fatkins D]]
-[[Category: Hawse, W F.]]
+[[Category: Hawse WF]]
-[[Category: Hoff, K G.]]
+[[Category: Hoff KG]]
-[[Category: Schramm, V L.]]
+[[Category: Schramm VL]]
-[[Category: Wolberger, C.]]
+[[Category: Wolberger C]]
-[[Category: Zheng, W.]]
+[[Category: Zheng W]]
-[[Category: Zubkova, O V.]]
+[[Category: Zubkova OV]]
-[[Category: Cytoplasm]]
-[[Category: Hydrolase]]
-[[Category: Metal-binding]]
-[[Category: Nad]]
-[[Category: Nad dependent deacetylase]]
-[[Category: Rossmann fold]]
-[[Category: Zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct  1 21:42:17 2008''