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: 99.57 kDa 
• Atom Count: 6749 
• Residue Count: 826 
• Unique protein chains: 1

4MWS

Crystal structure of human PPCA (trigonal crystal form 1)

• DOI: 10.2210/pdb4MWS/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-09-25 Released: 2014-03-12 
• Deposition Author(s): Kolli, N., Garman, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.146 
• R-Value Observed: 0.149 

Literature

Proteolytic activation of human cathepsin A.

Kolli, N., Garman, S.C.

(2014) J Biol Chem 289: 11592-11600

• PubMed: 24599961 
• DOI: 10.1074/jbc.M113.524280
• Primary Citation of Related Structures:  
  4MWS, 4MWT


• PubMed Abstract: 
  

Galactosialidosis is a human lysosomal storage disease caused by deficiency in the multifunctional lysosomal protease cathepsin A (also known as protective protein/cathepsin A, PPCA, catA, HPP, and CTSA; EC 3.4.16.5). Previous structural work on the inactive precursor human cathepsin A (zymogen) led to a two-stage model for activation, where proteolysis of a 1.6-kDa excision peptide is followed by a conformational change in a blocking peptide occluding the active site. Here we present evidence for an alternate model of activation of human cathepsin A, needing only cleavage of a 3.3-kDa excision peptide to yield full enzymatic activity, with no conformational change required. We present x-ray crystallographic, mass spectrometric, amino acid sequencing, enzymatic, and cellular data to support the cleavage-only activation model. The results clarify a longstanding question about the mechanism of cathepsin A activation and point to new avenues for the design of mechanism-based inhibitors of the enzyme.

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Organizational Affiliation: 

From the Department of Biochemistry and Molecular Biology and.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysosomal protective protein	A, B	428	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
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.146 
• R-Value Observed: 0.149 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.889	α = 90
b = 134.889	β = 90
c = 99.805	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-25 
• Released Date: 2014-03-12 
Deposition Author(s): Kolli, N., Garman, S.C.

Revision History 

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary