3gjs: Difference between revisions

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-[[Image:3gjs.png|left|200px]]
-<!--
+==Caspase-3 Binds Diverse P4 Residues in Peptides==
-The line below this paragraph, containing "STRUCTURE_3gjs", creates the "Structure Box" on the page.
+<StructureSection load='3gjs' size='340' side='right'caption='[[3gjs]], [[Resolution|resolution]] 1.90&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'>[[3gjs]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GJS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GJS FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ASJ:(3S)-3-AMINO-4-HYDROXYBUTANOIC+ACID'>ASJ</scene></td></tr>
--->
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gjq|3gjq]], [[3gjr|3gjr]], [[3gjt|3gjt]]</div></td></tr>
-{{STRUCTURE_3gjs|  PDB=3gjs  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CASP3, CPP32 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Caspase-3 Caspase-3], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.56 3.4.22.56] </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=3gjs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gjs OCA], [https://pdbe.org/3gjs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gjs RCSB], [https://www.ebi.ac.uk/pdbsum/3gjs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gjs ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/CASP3_HUMAN CASP3_HUMAN]] Involved in the activation cascade of caspases responsible for apoptosis execution. At the onset of apoptosis it proteolytically cleaves poly(ADP-ribose) polymerase (PARP) at a '216-Asp-|-Gly-217' bond. Cleaves and activates sterol regulatory element binding proteins (SREBPs) between the basic helix-loop-helix leucine zipper domain and the membrane attachment domain. Cleaves and activates caspase-6, -7 and -9. Involved in the cleavage of huntingtin. Triggers cell adhesion in sympathetic neurons through RET cleavage.<ref>PMID:7596430</ref> <ref>PMID:21357690</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/gj/3gjs_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=3gjs ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Caspase-3 recognition of various P4 residues in its numerous protein substrates was investigated by crystallography, kinetics, and calculations on model complexes. Asp is the most frequent P4 residue in peptide substrates, although a wide variety of P4 residues are found in the cellular proteins cleaved by caspase-3. The binding of peptidic inhibitors with hydrophobic P4 residues, or no P4 residue, is illustrated by crystal structures of caspase-3 complexes with Ac-IEPD-Cho, Ac-WEHD-Cho, Ac-YVAD-Cho, and Boc-D(OMe)-Fmk at resolutions of 1.9-2.6 A. The P4 residues formed favorable hydrophobic interactions in two separate hydrophobic regions of the binding site. The side chains of P4 Ile and Tyr form hydrophobic interactions with caspase-3 residues Trp206 and Trp214 within a non-polar pocket of the S4 subsite, while P4 Trp interacts with Phe250 and Phe252 that can also form the S5 subsite. These interactions of hydrophobic P4 residues are distinct from those for polar P4 Asp, which indicates the adaptability of caspase-3 for binding diverse P4 residues. The predicted trends in peptide binding from molecular models had high correlation with experimental values for peptide inhibitors. Analysis of structural models for the binding of 20 different amino acids at P4 in the aldehyde peptide Ac-XEVD-Cho suggested that the majority of hydrophilic P4 residues interact with Phe250, while hydrophobic residues interact with Trp206, Phe250, and Trp214. Overall, the S4 pocket of caspase-3 exhibits flexible adaptation for different residues and the new structures and models, especially for hydrophobic P4 residues, will be helpful for the design of caspase-3 based drugs.
-===Caspase-3 Binds Diverse P4 Residues in Peptides===
+Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling.,Fang B, Fu G, Agniswamy J, Harrison RW, Weber IT Apoptosis. 2009 Mar 13. PMID:19283487<ref>PMID:19283487</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_19283487}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3gjs" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19283487 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19283487}}
-==About this Structure==
-[[3gjs]] is a 6 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=3GJS OCA].
 ==See Also==
-*[[Caspase]]
+*[[Caspase 3D structures|Caspase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019283487</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Caspase-3]]
-[[Category: Homo sapiens]]
+[[Category: Human]]
-[[Category: Agniswamy, J.]]
+[[Category: Large Structures]]
-[[Category: Fang, B.]]
+[[Category: Agniswamy, J]]
-[[Category: Fu, G.]]
+[[Category: Fang, B]]
-[[Category: Harrison, R W.]]
+[[Category: Fu, G]]
-[[Category: Weber, I T.]]
+[[Category: Harrison, R W]]
+[[Category: Weber, I T]]
 [[Category: Apoptosis]]
 [[Category: Cysteine protease]]