2ZPS

Crystal structure of anionic trypsin isoform 3 from chum salmon

Summary for 2ZPS

• Entry DOI: 10.2210/pdb2zps/pdb
• Related: 2ZPQ 2ZPR
• Descriptor: Anionic trypsin, CALCIUM ION, BENZAMIDINE, ... (4 entities in total)
• Functional Keywords: serine proteinase, trypsin, hydrolase, protease, serine protease
• Biological source: Oncorhynchus keta (Chum salmon)
• Total number of polymer chains: 1
• Total formula weight: 24051.10

Authors

Iyaguchi, D.,Toyota, E. (deposition date: 2008-07-28, release date: 2009-07-28, Last modification date: 2024-10-30)

Primary citation

Toyota, E.,Iyaguchi, D.,Sekizaki, H.,Tateyama, M.,Ng, K.K.
A structural comparison of three isoforms of anionic trypsin from chum salmon (Oncorhynchus keta).
Acta Crystallogr.,Sect.D, 65:717-723, 2009

PubMed Abstract: Three anionic salmon trypsin isoforms (CST-1, CST-2 and CST-3) were isolated from the pyloric caeca of chum salmon (Oncorhynchus keta). The order of catalytic efficiency (K(m)/k(cat)) of the isoforms during BAPA hydrolysis was CST-2 > CST-1 > CST-3. In order to find a structural rationalization for the observed difference in catalytic efficiency, the X-ray crystallographic structures of the three isoforms were compared in detail. Some structural differences were observed in the C-terminal alpha-helix, interdomain loop and active-site region. From the results of the detailed comparison, it appears that the structural flexibility of the C-terminal alpha-helix, which interacts with the N-terminal domain, and the substrate-binding pocket in CST-3 are lower than those in CST-1 and CST-2. In addition, the conformation of the catalytic triad (His57, Asp102 and Ser195) differs among the three isoforms. The imidazole N atom of His57 in CST-1 and CST-2 forms a hydrogen bond to the hydroxyl O atom of Ser195, but the distance between the imidazole N atom of His57 and the hydroxyl O atom of Ser195 in CST-3 is too great (3.8 A) for the formation of a hydrogen bond. Thus, the nucleophilicity of the hydroxyl group of Ser195 in CST-3 is weaker than that in CST-1 or CST-2. Furthermore, the electrostatic potential of the substrate-binding pocket in CST-2 is markedly lower than those in CST-1 and CST-3 owing to the negative charges of Asp150, Asp153 and Glu221B that arise from the long-range effect. These results may explain the higher catalytic efficiency of CST-2 compared with CST-1 and CST-3.

PubMed: 19564692
DOI: 10.1107/S0907444909012165

Experimental method

X-RAY DIFFRACTION (1.55 Å)