1IWD

Proposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal Structure of a Plant Cysteine Protease Ervatamin B: Insight into the Structural Basis of its Stability and Substrate Specificity.

Summary for 1IWD

• Entry DOI: 10.2210/pdb1iwd/pdb
• Descriptor: ERVATAMIN B, THIOSULFATE (3 entities in total)
• Functional Keywords: cysteine protease, alpha-beta protein, catalytic dyad, l-domain, r-domain., hydrolase
• Biological source: Tabernaemontana divaricata
• Total number of polymer chains: 1
• Total formula weight: 23312.93

Authors

Chakrabarti, C.,Biswas, S.,Dattagupta, J.K. (deposition date: 2002-05-02, release date: 2003-05-06, Last modification date: 2023-10-25)

Primary citation

Biswas, S.,Chakrabarti, C.,Kundu, S.,Jagannadham, M.V.,Dattagupta, J.K.
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, 2003

PubMed Abstract: 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.

PubMed: 12784208
DOI: 10.1002/prot.10319

Experimental method

X-RAY DIFFRACTION (1.63 Å)