This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3edq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:01, 30 August 2023) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3edq.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of Caspase-3 with inhibitor AC-LDESD-CHO==
-
The line below this paragraph, containing "STRUCTURE_3edq", creates the "Structure Box" on the page.
+
<StructureSection load='3edq' size='340' side='right'caption='[[3edq]], [[Resolution|resolution]] 1.61&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'>[[3edq]] is a 6 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=3EDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EDQ 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]] 1.61&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ASA:ASPARTIC+ALDEHYDE'>ASA</scene></td></tr>
-
{{STRUCTURE_3edq| PDB=3edq | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3edq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3edq OCA], [https://pdbe.org/3edq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3edq RCSB], [https://www.ebi.ac.uk/pdbsum/3edq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3edq 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/ed/3edq_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=3edq ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Caspase-3, -6 and -7 cleave many proteins at specific sites to induce apoptosis. Their recognition of the P5 position in substrates has been investigated by kinetics, modeling and crystallography. Caspase-3 and -6 recognize P5 in pentapeptides as shown by enzyme activity data and interactions observed in the crystal structure of caspase-3/LDESD and in a model for caspase-6. In caspase-3 the P5 main-chain was anchored by interactions with Ser209 in loop-3 and the P5 Leu side-chain interacted with Phe250 and Phe252 in loop-4 consistent with 50% increased hydrolysis of LDEVD relative to DEVD. Caspase-6 formed similar interactions and showed a preference for polar P5 in QDEVD likely due to interactions with polar Lys265 and hydrophobic Phe263 in loop-4. Caspase-7 exhibited no preference for P5 residue in agreement with the absence of P5 interactions in the caspase-7/LDESD crystal structure. Initiator caspase-8, with Pro in the P5-anchoring position and no loop-4, had only 20% activity on tested pentapeptides relative to DEVD. Therefore, caspases-3 and -6 bind P5 using critical loop-3 anchoring Ser/Thr and loop-4 side-chain interactions, while caspase-7 and -8 lack P5-binding residues.
-
===Crystal structure of Caspase-3 with inhibitor AC-LDESD-CHO===
+
Structural basis for executioner caspase recognition of P5 position in substrates.,Fu G, Chumanevich AA, Agniswamy J, Fang B, Harrison RW, Weber IT Apoptosis. 2008 Nov;13(11):1291-302. PMID:18780184<ref>PMID:18780184</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3edq" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18780184}}, adds the Publication Abstract to the page
+
*[[Caspase 3D structures|Caspase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18780184 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18780184}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
3EDQ is a [[Protein complex]] structure of sequences 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=3EDQ OCA].
+
-
 
+
-
==Reference==
+
-
Structural basis for executioner caspase recognition of P5 position in substrates., Fu G, Chumanevich AA, Agniswamy J, Fang B, Harrison RW, Weber IT, Apoptosis. 2008 Nov;13(11):1291-302. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18780184 18780184]
+
-
[[Category: Caspase-3]]
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Protein complex]]
+
[[Category: Large Structures]]
-
[[Category: Fu, G.]]
+
[[Category: Fu G]]
-
[[Category: Apoptosis]]
+
-
[[Category: Cysteine protease]]
+
-
[[Category: Cytoplasm]]
+
-
[[Category: Enzyme catalysis]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Induced fit]]
+
-
[[Category: Phosphoprotein]]
+
-
[[Category: Polymorphism]]
+
-
[[Category: Protease]]
+
-
[[Category: S-nitrosylation]]
+
-
[[Category: Thiol protease]]
+
-
[[Category: Zymogen]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 29 11:00:57 2008''
+

Current revision

Crystal structure of Caspase-3 with inhibitor AC-LDESD-CHO

PDB ID 3edq

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3edq"
Personal tools