1JQP

dipeptidyl peptidase I (cathepsin C), a tetrameric cysteine protease of the papain family

• PDB DOI: https://doi.org/10.2210/pdb1JQP/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2001-08-08 Released: 2002-10-18 
• Deposition Author(s): Olsen, J.G., Kadziola, A., Lauritzen, C., Pedersen, J., Larsen, S., Dahl, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.245 

Literature

Tetrameric dipeptidyl peptidase I directs substrate specificity by use of the residual pro-part domain

Olsen, J.G., Kadziola, A., Lauritzen, C., Pedersen, J., Larsen, S., Dahl, S.W.

(2001) FEBS Lett 506: 201-206

• PubMed: 11602245 
• DOI: https://doi.org/10.1016/s0014-5793(01)02911-8
• Primary Citation of Related Structures:  
  1JQP


• PubMed Abstract: 
  

  The crystal structure of mature dipeptidyl peptidase I reveals insight into the unique tetrameric structure, substrate binding and activation of this atypical papain family peptidase. Each subunit is composed of three peptides. The heavy and light chains form the catalytic domain, which adopts the papain fold. The residual pro-part forms a beta-barrel with the carboxylate group of Asp1 pointing towards the substrate amino-terminus. The tetrameric structure appears to stabilize the association of the two domains and encloses a 12700 A3 spherical cavity. The tetramer contains six chloride ions, one buried in each S2 pocket and two at subunit interfaces.

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Organizational Affiliation: 

Center for Crystallographic Studies, University of Copenhagen, Denmark.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.44 kDa 
• Atom Count: 2,898 
• Modelled Residue Count: 348 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dipeptidyl peptidase I	A	438	Rattus norvegicus	Mutation(s): 0  EC: 3.4.14.1
UniProt
Find proteins for P80067 (Rattus norvegicus) Explore P80067  Go to UniProtKB:  P80067
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P80067-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.245 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.24	α = 90
b = 166.24	β = 90
c = 80.48	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-18 
Deposition Author(s): Olsen, J.G., Kadziola, A., Lauritzen, C., Pedersen, J., Larsen, S., Dahl, S.W.

Revision History  

• Version 1.0: 2002-10-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-02-14
  Changes: Data collection, Experimental preparation
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary