Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 53.44 kDa 
• Atom Count: 4275 
• Residue Count: 413 
• Unique protein chains: 1

4CIB

crystal structure of cathepsin a, complexed with compound 2

• DOI: 10.2210/pdb4CIB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-12-06 Released: 2014-02-26 
• Deposition Author(s): Schreuder, H.A., Liesum, A., Kroll, K., Boehnisch, B., Buning, C., Ruf, S., Buning, C., Sadowski, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.211 
• R-Value Work: 0.141 
• R-Value Observed: 0.145 

Literature

Crystal structure of cathepsin A, a novel target for the treatment of cardiovascular diseases.

Schreuder, H.A., Liesum, A., Kroll, K., Bohnisch, B., Buning, C., Ruf, S., Sadowski, T.

(2014) Biochem Biophys Res Commun 445: 451-456

• PubMed: 24530914 
• DOI: 10.1016/j.bbrc.2014.02.014
• Primary Citation of Related Structures:  
  4CI9, 4CIB, 4CIA


• PubMed Abstract: 
  

The lysosomal serine carboxypeptidase cathepsin A is involved in the breakdown of peptide hormones like endothelin and bradykinin. Recent pharmacological studies with cathepsin A inhibitors in rodents showed a remarkable reduction in cardiac hypertrophy and atrial fibrillation, making cathepsin A a promising target for the treatment of heart failure. Here we describe the crystal structures of activated cathepsin A without inhibitor and with two compounds that mimic the tetrahedral intermediate and the reaction product, respectively. The structure of activated cathepsin A turned out to be very similar to the structure of the inactive precursor. The only difference was the removal of a 40 residue activation domain, partially due to proteolytic removal of the activation peptide, and partially by an order-disorder transition of the peptides flanking the removed activation peptide. The termini of the catalytic core are held together by the Cys253-Cys303 disulfide bond, just before and after the activation domain. One of the compounds we soaked in our crystals reacted covalently with the catalytic Ser150 and formed a tetrahedral intermediate. The other compound got cleaved by the enzyme and a fragment, resembling one of the natural reaction products, was found in the active site. These studies establish cathepsin A as a classical serine proteinase with a well-defined oxyanion hole. The carboxylate group of the cleavage product is bound by a hydrogen-bonding network involving one aspartate and two glutamate side chains. This network can only form if at least half of the carboxylate groups involved are protonated, which explains the acidic pH optimum of the enzyme.

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Related Citations: 

• Novel Beta-Amino Acid Derivatives as Inhibitors of Cathepsin A.
  Ruf, S., Buning, C., Schreuder, H., Horstick, G., Linz, W., Olpp, T., Pernerstorfer, J., Hiss, K., Kroll, K., Kannt, A., Kohlmann, M., Linz, D., Hubschle, T., Rutten, H., Wirth, K., Schmidt, T., Sadowski, T.
  (2012) J Med Chem 55: 7636

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Organizational Affiliation: 

Sanofi-Aventis Pharma Deutschland GmbH, Industriepark Höchst, 65926 Frankfurt am Main, Germany. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOSOMAL PROTECTIVE PROTEIN	A	455	Homo sapiens	Mutation(s): 0  Gene Names: CTSA, PPGB EC: 3.4.16.5
Find proteins for P10619 (Homo sapiens) Explore P10619  Go to UniProtKB:  P10619
NIH Common Fund Data Resources
PHAROS:  P10619 GTEx:  ENSG00000064601

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7UZ	A	2-(cyclohexylmethyl)propanedioic acid C10 H16 O4 PYKSXWASTAWCSS-UHFFFAOYSA-N
CD	A	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.211 
• R-Value Work: 0.141 
• R-Value Observed: 0.145 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.649	α = 90
b = 102.527	β = 100.94
c = 49.395	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-06 
• Released Date: 2014-02-26 
Deposition Author(s): Schreuder, H.A., Liesum, A., Kroll, K., Boehnisch, B., Buning, C., Ruf, S., Buning, C., Sadowski, T.

Revision History 

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2014-04-02
  Changes: Database references
• Version 1.2: 2019-03-13
  Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary