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.

1s4v

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:59, 8 March 2018

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

Structural highlights

1s4v is a 4 chain structure with sequence from Ricinus communis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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 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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Than ME, Helm M, Simpson DJ, Lottspeich F, Huber R, Gietl C. The 2.0 A crystal structure and substrate specificity of the KDEL-tailed cysteine endopeptidase functioning in programmed cell death of Ricinus communis endosperm. J Mol Biol. 2004 Mar 5;336(5):1103-16. PMID:15037072 doi:10.1016/j.jmb.2003.12.075

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1s4v"

@@ Line 1: / Line 1: @@
 ==The 2.0 A crystal structure of the KDEL-tailed cysteine endopeptidase functioning in programmed cell death of Ricinus communis endosperm==
 <StructureSection load='1s4v' size='340' side='right' caption='[[1s4v]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0QE:CHLOROMETHANE'>0QE</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1s4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s4v OCA], [http://pdbe.org/1s4v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s4v RCSB], [http://www.ebi.ac.uk/pdbsum/1s4v PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1s4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s4v OCA], [http://pdbe.org/1s4v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s4v RCSB], [http://www.ebi.ac.uk/pdbsum/1s4v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s4v ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s4/1s4v_consurf.spt"</scriptWhenChecked>
+    <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/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1s4v

From Proteopedia

Revision as of 06:59, 8 March 2018

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

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox