Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.08 kDa 
• Atom Count: 3790 
• Modelled Residue Count: 458 
• Deposited Residue Count: 466 
• Unique protein chains: 2

1S4V

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

• PDB DOI: 10.2210/pdb1S4V/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Ricinus communis
• Mutation(s): No 


• Deposited: 2004-01-19 Released: 2004-03-16 
• Deposition Author(s): Than, M.E., Helm, M., Simpson, D.J., Lottspeich, F., Huber, R., Gietl, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Literature

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, M.E., Helm, M., Simpson, D.J., Lottspeich, F., Huber, R., Gietl, C.

(2004) J Mol Biol 336: 1103-1116

• PubMed: 15037072 
• DOI: 10.1016/j.jmb.2003.12.075
• Primary Citation of Related Structures:  
  1S4V


• 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.

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Organizational Affiliation: 

Max-Plank-Institut für Biochemie, Abteilung Strukturforschung, D-82152 Martinsried, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cysteine endopeptidase	A, B	229	Ricinus communis	Mutation(s): 0  Gene Names: CYSEP EC: 3.4.22
UniProt
Find proteins for O65039 (Ricinus communis) Explore O65039  Go to UniProtKB:  O65039

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DVA-LEU-LYS-0QE peptide	C, D	4	Ricinus communis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000286	C, D	D-valyl-N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-L-leucinamide	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.448	α = 90
b = 68.162	β = 90
c = 163.78	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-19 
• Released Date: 2004-03-16 
Deposition Author(s): Than, M.E., Helm, M., Simpson, D.J., Lottspeich, F., Huber, R., Gietl, C.

Revision History  

• Version 1.0: 2004-03-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other