1s4v

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (00:28, 21 November 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1s4v.png|left|200px]]
 
-
<!--
+
==The 2.0 A crystal structure of the KDEL-tailed cysteine endopeptidase functioning in programmed cell death of Ricinus communis endosperm==
-
The line below this paragraph, containing "STRUCTURE_1s4v", creates the "Structure Box" on the page.
+
<StructureSection load='1s4v' size='340' side='right'caption='[[1s4v]], [[Resolution|resolution]] 2.00&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'>[[1s4v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S4V 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&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0QE:CHLOROMETHANE'>0QE</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_1s4v| PDB=1s4v | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s4v OCA], [https://pdbe.org/1s4v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s4v RCSB], [https://www.ebi.ac.uk/pdbsum/1s4v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s4v ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/CYSEP_RICCO CYSEP_RICCO] Involved in programmed cell death. Shows a pronounced preference for hydrophobic residues in the P2 position and no obvious preference in the P1 position of the cleavage site. Accepts proline at the P1 and P1' positions.
 +
== 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/s4/1s4v_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=1s4v ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
In the senescing endosperm of germinating castor bean (Ricinus communis) a special organelle (the ricinosome) releases a papain-type cysteine endopeptidase (CysEP) during the final stages of cellular disintegration. Protein cleavage sites for the Ricinus CysEP were determined with fluorogenic peptides (Abz-Xaa-Arg-/-Gln-Gln-Tyr(NO2)-Asp). The highest kcat/Km values were obtained with neutral amino acid residues with large aliphatic and non-polar (Leu, Val, Ile, Met) or aromatic (Phe, Tyr, Trp) side-chains. A second series (Abz-Leu-Xaa-/Gln-Pro-Tyr(NO2)-Asp) was evaluated. Based on these results, the covalent binding inhibitor H-D-Val-Leu-Lys-chloromethylketone (CMK) was chosen as substrate analogue for replacement in the catalytic site. Unusually, CysEP cleaved beta-casein N and C-terminal to the amino acid proline. CysEP was crystallized, its structure was solved by molecular replacement at 2.0 A resolution and refined to a R-factor of 18.1% (Rfree=22.6%). The polypeptide chain folds as in papain into two domains divided by the active site cleft, an elongated surface depression harboring the active site. The non-primed specificity subsites of the proteinase are clearly defined by the H-D-Val-Leu-Lys-CMK-inhibitor covalently bound to the active site. The absence of the occluding loop, which blocks the active site of exopeptidases at the C-terminal side of the scissile bond, identifies CysEP as an endopeptidase. The more open pocket of the Ricinus CysEP correlates with the extended variety of substrate amino acid residues accommodated by this enzyme, including even proline at the P1 and P1' positions. This may allow the enzyme to attack a greater variety of proteins during programmed cell death.
-
===The 2.0 A crystal structure of the KDEL-tailed cysteine endopeptidase functioning in programmed cell death of Ricinus communis endosperm===
+
The 2.0 A crystal structure and substrate specificity of the KDEL-tailed cysteine endopeptidase functioning in programmed cell death of Ricinus communis endosperm.,Than ME, Helm M, Simpson DJ, Lottspeich F, Huber R, Gietl C J Mol Biol. 2004 Mar 5;336(5):1103-16. PMID:15037072<ref>PMID:15037072</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_15037072}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1s4v" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 15037072 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_15037072}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
1S4V is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S4V OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:15037072</ref><references group="xtra"/>
+
[[Category: Ricinus communis]]
[[Category: Ricinus communis]]
-
[[Category: Gietl, C.]]
+
[[Category: Gietl C]]
-
[[Category: Helm, M.]]
+
[[Category: Helm M]]
-
[[Category: Huber, R.]]
+
[[Category: Huber R]]
-
[[Category: Lottspeich, F.]]
+
[[Category: Lottspeich F]]
-
[[Category: Simpson, D J.]]
+
[[Category: Simpson DJ]]
-
[[Category: Than, M E.]]
+
[[Category: Than ME]]
-
[[Category: Endosperm]]
+
-
[[Category: Kdel er retention signal]]
+
-
[[Category: Ricinosome]]
+
-
[[Category: Seed germination]]
+
-
[[Category: Senescence]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:33:05 2009''
+

Current revision

The 2.0 A crystal structure of the KDEL-tailed cysteine endopeptidase functioning in programmed cell death of Ricinus communis endosperm

PDB ID 1s4v

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/1s4v"
Personal tools