5N7N

CRYSTAL STRUCTURE OF CATHEPSIN D ZYMOGEN FROM THE TICK IXODES RICINUS (IRCD1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.chembiol.2018.01.001
  • Primary Citation of Related Structures:  
    5N70, 5N71, 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.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, 12840 Prague, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative cathepsin d
A, B, C, D
367Ixodes ricinusMutation(s): 0 
UniProt
Find proteins for V5HCK7 (Ixodes ricinus)
Explore V5HCK7 
Go to UniProtKB:  V5HCK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5HCK7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
U [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NH4
Query on NH4

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B],
T [auth C],
Z [auth D]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.322α = 90
b = 94.981β = 99.28
c = 106.17γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Advisory, Database references
  • Version 1.2: 2018-03-28
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary