Biological Assembly 1  

 3D View: Structure | Electron Density

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 | Electron Density

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

Macromolecule Content

• Total Structure Weight: 38.59 kDa 
• Atom Count: 2749 
• Residue Count: 347 
• Unique protein chains: 2

5N70

CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) IN COMPLEX WITH THE N-TERMINAL OCTAPEPTIDE OF THE PROPEPTID

• DOI: 10.2210/pdb5N70/pdb

• Classification: HYDROLASE
• Organism(s): Ixodes ricinus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-02-17 Released: 2017-12-27 
• Deposition Author(s): Brynda, J., Hanova, I., Hobizalova, R., Mares, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.231 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite.

Hanova, I., Brynda, J., Houstecka, R., Alam, N., Sojka, D., Kopacek, P., Maresova, L., Vondrasek, J., Horn, M., Schueler-Furman, O., Mares, M.

(2018) Cell Chem Biol 25: 318-329.e4

• PubMed: 29396291 
• DOI: 10.1016/j.chembiol.2018.01.001
• Primary Citation of Related Structures:  
  5N71, 5N70, 5N7N, 5N7Q


• PubMed Abstract: 
  

Pepsin-family aspartic peptidases are biosynthesized as inactive zymogens in which the propeptide blocks the active site until its proteolytic removal upon enzyme activation. Here, we describe a novel dual regulatory function for the propeptide using a set of crystal structures of the parasite cathepsin D IrCD1. In the IrCD1 zymogen, intramolecular autoinhibition by the intact propeptide is mediated by an evolutionarily conserved exosite on the enzyme core. After activation, the mature enzyme employs the same exosite to rebind a small fragment derived from the cleaved propeptide. This fragment functions as an effective natural inhibitor of mature IrCD1 that operates in a pH-dependent manner through a unique allosteric inhibition mechanism. The study uncovers the propeptide-binding exosite as a target for the regulation of pepsin-family aspartic peptidases and defines the structural requirements for exosite inhibition.

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Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cathepsin d	A	345	Ixodes ricinus	Mutation(s): 0
Find proteins for V5HCK7 (Ixodes ricinus) Explore V5HCK7  Go to UniProtKB:  V5HCK7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-PHE-ARG-ILE-PRO-LEU-THR-ARG	B	8	Ixodes ricinus	Mutation(s): 0
Find proteins for A4GTA5 (Ixodes ricinus) Explore A4GTA5  Go to UniProtKB:  A4GTA5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.231 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.925	α = 90
b = 63.925	β = 90
c = 80.496	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-02-17 
• Released Date: 2017-12-27 
Deposition Author(s): Brynda, J., Hanova, I., Hobizalova, R., Mares, M.

Revision History 

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2018-02-28
  Changes: Database references
• Version 1.2: 2018-03-28
  Changes: Database references