Crystal structure of a papain-like cysteine protease Ervatamin-A complexed with irreversible inhibitor E-64

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

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Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria

Ghosh, R.Chakraborty, S.Chakrabarti, C.Dattagupta, J.K.Biswas, S.

(2008) FEBS J 275: 421-434

  • DOI: https://doi.org/10.1111/j.1742-4658.2007.06211.x
  • Primary Citation of Related Structures:  
    2PRE, 3BCN

  • PubMed Abstract: 

    Multiple proteases of the same family are quite often present in the same species in biological systems. These multiple proteases, despite having high homology in their primary and tertiary structures, show deviations in properties such as stability, activity, and specificity. It is of interest, therefore, to compare the structures of these multiple proteases in a single species to identify the structural changes, if any, that may be responsible for such deviations. Ervatamin-A, ervatamin-B and ervatamin-C are three such papain-like cysteine proteases found in the latex of the tropical plant Ervatamia coronaria, and are known not only for their high stability over a wide range of temperature and pH, but also for variations in activity and specificity among themselves and among other members of the family. Here we report the crystal structures of ervatamin-A and ervatamin-C, complexed with an irreversible inhibitor 1-[l-N-(trans-epoxysuccinyl)leucyl]amino-4-guanidinobutane (E-64), together with enzyme kinetics and molecular dynamic simulation studies. A comparison of these results with the earlier structures helps in a correlation of the structural features with the corresponding functional properties. The specificity constants (k(cat)/K(m)) for the ervatamins indicate that all of these enzymes have specificity for a branched hydrophobic residue at the P2 position of the peptide substrates, with different degrees of efficiency. A single amino acid change, as compared to ervatamin-C, in the S2 pocket of ervatamin-A (Ala67-->Tyr) results in a 57-fold increase in its k(cat)/K(m) value for a substrate having a Val at the P2 position. Our studies indicate a higher enzymatic activity of ervatamin-A, which has been subsequently explained at the molecular level from the three-dimensional structure of the enzyme and in the context of its helix polarizibility and active site plasticity.

  • Organizational Affiliation

    Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
209Tabernaemontana divaricataMutation(s): 0 
EC: 3.4.22
Find proteins for A5YVK8 (Tabernaemontana divaricata)
Explore A5YVK8 
Go to UniProtKB:  A5YVK8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5YVK8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on E64

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C15 H30 N5 O5
Query on BME

Download Ideal Coordinates CCD File 
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
E64 PDBBind:  3BCN IC50: 76.25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.168α = 90
b = 105.587β = 101.96
c = 73.927γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AUTOMARdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description