PDBsum entry 1iwd

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Hydrolase PDB id
Protein chain
215 a.a. *
Waters ×208
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Proposed amino acid sequence and the 1.63 angstrom x-ray cry structure of a plant cysteine protease ervatamin b: insight structural basis of its stability and substrate specificity
Structure: Ervatamin b. Chain: a
Source: Tabernaemontana divaricata. Organism_taxid: 52861
1.63Å     R-factor:   0.161     R-free:   0.184
Authors: C.Chakrabarti,S.Biswas,J.K.Dattagupta
Key ref:
S.Biswas et al. (2003). Proposed amino acid sequence and the 1.63 A X-ray crystal structure of a plant cysteine protease, ervatamin B: some insights into the structural basis of its stability and substrate specificity. Proteins, 51, 489-497. PubMed id: 12784208 DOI: 10.1002/prot.10319
02-May-02     Release date:   06-May-03    
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Protein chain
Pfam   ArchSchema ?
P60994  (ERVB_TABDI) -  Ervatamin-B
215 a.a.
215 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     hydrolase activity     3 terms  


DOI no: 10.1002/prot.10319 Proteins 51:489-497 (2003)
PubMed id: 12784208  
Proposed amino acid sequence and the 1.63 A X-ray crystal structure of a plant cysteine protease, ervatamin B: some insights into the structural basis of its stability and substrate specificity.
S.Biswas, C.Chakrabarti, S.Kundu, M.V.Jagannadham, J.K.Dattagupta.
The crystal structure of a cysteine protease ervatamin B, isolated from the medicinal plant Ervatamia coronaria, has been determined at 1.63 A. The unknown primary structure of the enzyme could also be traced from the high-quality electron density map. The final refined model, consisting of 215 amino acid residues, 208 water molecules, and a thiosulfate ligand molecule, has a crystallographic R-factor of 15.9% and a free R-factor of 18.2% for F > 2sigma(F). The protein belongs to the papain superfamily of cysteine proteases and has some unique properties compared to other members of the family. Though the overall fold of the structure, comprising two domains, is similar to the others, a few natural substitutions of conserved amino acid residues at the interdomain cleft of ervatamin B are expected to increase the stability of the protein. The substitution of a lysine residue by an arginine (residue 177) in this region of the protein may be important, because Lys --> Arg substitution is reported to increase the stability of proteins. Another substitution in this cleft region that helps to hold the domains together through hydrogen bonds is Ser36, replacing a conserved glycine residue in the others. There are also some substitutions in and around the active site cleft. Residues Tyr67, Pro68, Val157, and Ser205 in papain are replaced by Trp67, Met68, Gln156, and Leu208, respectively, in ervatamin B, which reduces the volume of the S2 subsite to almost one-fourth that of papain, and this in turn alters the substrate specificity of the enzyme.
  Selected figure(s)  
Figure 6.
Figure 6. The water channel in the interdomain cleft near the substituted residues Arg177 and Ser36. The figure was prepared by Insight II (MSI, Inc.).
Figure 7.
Figure 7. Superposition of the S2 subsites of ervatamin B (red) and papain (green). The substrate analog inhibitor ZPACK, with a phenyl ring at its P2 position, is shown in blue.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 51, 489-497) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20304972 D.Choudhury, S.Biswas, S.Roy, and J.K.Dattagupta (2010).
Improving thermostability of papain through structure-based protein engineering.
  Protein Eng Des Sel, 23, 457-467.  
18167146 R.Ghosh, S.Chakraborty, C.Chakrabarti, J.K.Dattagupta, and S.Biswas (2008).
Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria.
  FEBS J, 275, 421-434.
PDB codes: 2pre 2psc 3bcn
  16511096 S.Chakraborty, S.Biswas, C.Chakrabarti, and J.K.Dattagupta (2005).
Crystallization and preliminary X-ray diffraction studies of the cysteine protease ervatamin A from Ervatamia coronaria.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 562-564.  
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