1S4V

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

Summary for 1S4V

• Entry DOI: 10.2210/pdb1s4v/pdb
• Related PRD ID: PRD_000286
• Descriptor: cysteine endopeptidase, DVA-LEU-LYS-0QE peptide, SULFATE ION, ... (4 entities in total)
• Functional Keywords: kdel er retention signal, endosperm, ricinosomes, seed germination, senescence, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Ricinus communis (castor bean); More
• Total number of polymer chains: 4
• Total formula weight: 50078.21

Authors

Than, M.E.,Helm, M.,Simpson, D.J.,Lottspeich, F.,Huber, R.,Gietl, C. (deposition date: 2004-01-19, release date: 2004-03-16, Last modification date: 2024-11-20)

Primary citation

Than, M.E.,Helm, M.,Simpson, D.J.,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., 336:1103-1116, 2004

PubMed Abstract: 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.

PubMed: 15037072
DOI: 10.1016/j.jmb.2003.12.075

Experimental method

X-RAY DIFFRACTION (2 Å)