2ar9: Difference between revisions

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-[[Image:2ar9.png|left|200px]]
-<!--
+==Crystal structure of a dimeric caspase-9==
-The line below this paragraph, containing "STRUCTURE_2ar9", creates the "Structure Box" on the page.
+<StructureSection load='2ar9' size='340' side='right'caption='[[2ar9]], [[Resolution|resolution]] 2.80&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'>[[2ar9]] 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=2AR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AR9 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]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLT:D-MALATE'>MLT</scene></td></tr>
-{{STRUCTURE_2ar9|  PDB=2ar9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ar9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ar9 OCA], [https://pdbe.org/2ar9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ar9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ar9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ar9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CASP9_HUMAN CASP9_HUMAN] Involved in the activation cascade of caspases responsible for apoptosis execution. Binding of caspase-9 to Apaf-1 leads to activation of the protease which then cleaves and activates caspase-3. Promotes DNA damage-induced apoptosis in a ABL1/c-Abl-dependent manner. Proteolytically cleaves poly(ADP-ribose) polymerase (PARP).<ref>PMID:15657060</ref>   Isoform 2 lacks activity is an dominant-negative inhibitor of caspase-9.<ref>PMID:15657060</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/ar/2ar9_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/main_output.php?pdb_ID=2ar9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Caspases are responsible for the execution of programmed cell death (apoptosis) and must undergo proteolytic activation, in response to apoptotic stimuli, to function. The mechanism of initiator caspase activation has been generalized by the induced proximity model, which is thought to drive dimerization-mediated activation of caspases. The initiator caspase, caspase-9, exists predominantly as a monomer in solution. To examine the induced proximity model, we engineered a constitutively dimeric caspase-9 by relieving steric hindrance at the dimer interface. Crystal structure of the engineered caspase-9 closely resembles that of the wild-type (WT) caspase-9, including all relevant structural details and the asymmetric nature of two monomers. Compared to the WT caspase-9, this engineered dimer exhibits a higher level of catalytic activity in vitro and induces more efficient cell death when expressed. However, the catalytic activity of the dimeric caspase-9 is only a small fraction of that for the Apaf-1-activated caspase-9. Furthermore, in contrast to the WT caspase-9, the activity of the dimeric caspase-9 can no longer be significantly enhanced in an Apaf-1-dependent manner. These findings suggest that dimerization of caspase-9 may be qualitatively different from its activation by Apaf-1, and in conjunction with other evidence, posit an induced conformation model for the activation of initiator caspases.
-===Crystal structure of a dimeric caspase-9===
+Engineering a dimeric caspase-9: a re-evaluation of the induced proximity model for caspase activation.,Chao Y, Shiozaki EN, Srinivasula SM, Rigotti DJ, Fairman R, Shi Y PLoS Biol. 2005 Jun;3(6):e183. Epub 2005 May 10. PMID:15941357<ref>PMID:15941357</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_15941357}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ar9" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15941357 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_15941357}}
-==About this Structure==
-[[2ar9]] is a 4 chain structure of [[Caspase]] 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=2AR9 OCA].
 ==See Also==
-*[[Caspase]]
+*[[Caspase 3D structures|Caspase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015941357</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Chao, Y.]]
+[[Category: Large Structures]]
-[[Category: Fairman, R.]]
+[[Category: Chao Y]]
-[[Category: Rigotti, D J.]]
+[[Category: Fairman R]]
-[[Category: Shi, Y.]]
+[[Category: Rigotti DJ]]
-[[Category: Shiozaki, E N.]]
+[[Category: Shi Y]]
-[[Category: Srinivassula, S M.]]
+[[Category: Shiozaki EN]]
-[[Category: Caspase]]
+[[Category: Srinivassula SM]]
-[[Category: Caspase activation]]
-[[Category: Cysteine protease]]
-[[Category: Engineered caspase-9]]
-[[Category: Hydrolase]]
-[[Category: Initiator caspase]]