3TNX | pdb_00003tnx

Structure of the precursor of a thermostable variant of papain at 2.6 Angstroem resolution

• PDB DOI: https://doi.org/10.2210/pdb3TNX/pdb

• Classification: HYDROLASE
• Organism(s): Carica papaya
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-09-02 Released: 2012-09-12 
• Deposition Author(s): Roy, S., Choudhury, D., Dattagupta, J.K., Biswas, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.236 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

The structure of a thermostable mutant of pro-papain reveals its activation mechanism

Roy, S., Choudhury, D., Aich, P., Dattagupta, J.K., Biswas, S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1591-1603

• PubMed: 23151624 
• DOI: https://doi.org/10.1107/S0907444912038607
• Primary Citation Related Structures: 
  3TNX


• PubMed Abstract: 
  

  Papain is the archetype of a broad class of cysteine proteases (clan C1A) that contain a pro-peptide in the zymogen form which is required for correct folding and spatio-temporal regulation of proteolytic activity in the initial stages after expression. This study reports the X-ray structure of the zymogen of a thermostable mutant of papain at 2.6 Å resolution. The overall structure, in particular that of the mature part of the protease, is similar to those of other members of the family. The structure provides an explanation for the molecular basis of the maintenance of latency of the proteolytic activity of the zymogen by its pro-segment at neutral pH. The structural analysis, together with biochemical and biophysical studies, demonstrated that the pro-segment of the zymogen undergoes a rearrangement in the form of a structural loosening at acidic pH which triggers the proteolytic activation cascade. This study further explains the bimolecular stepwise autocatalytic activation mechanism by limited proteolysis of the zymogen of papain at the molecular level. The possible factors responsible for the higher thermal stability of the papain mutant have also been analyzed.

---

Organizational Affiliation: 
• Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 82.17 kDa 
• Atom Count: 5,079 
• Modeled Residue Count: 620 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain	A, B [auth C]	363	Carica papaya	Mutation(s): 4  EC: 3.4.22.2
UniProt
Find proteins for P00784 (Carica papaya) Explore P00784  Go to UniProtKB:  P00784

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.236 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.925	α = 90
b = 74.775	β = 93.03
c = 116.51	γ = 90

Software Package:

Software Name	Purpose
PX	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Roy, S., Choudhury, D., Dattagupta, J.K., Biswas, S.

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2012-09-19
  Changes: Database references
• Version 1.2: 2012-11-28
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary