PDBsum entry 2zpq

Hydrolase

PDB id: 2zpq

Contents

Protein chains

220 a.a. *

Ligands

SO4 ×2

BEN ×2

Metals

_CA ×2

Waters ×292

* Residue conservation analysis

PDB id:

2zpq

Name:

Hydrolase

Title:

Crystal structure of anionic trypsin isoform 1 from chum salmon

Structure:

Anionic trypsin. Chain: a, b

Source:

Oncorhynchus keta. Chum salmon. Organism_taxid: 8018

Resolution:

1.90Å R-factor: 0.193 R-free: 0.222

Authors:

D.Iyaguchi,E.Toyota

Key ref:

E.Toyota et al. (2009). A structural comparison of three isoforms of anionic trypsin from chum salmon (Oncorhynchus keta). Acta Crystallogr D Biol Crystallogr, 65, 717-723. PubMed id: 19564692 DOI: 10.1107/S0907444909012165

Date:

28-Jul-08 Release date: 28-Jul-09

Protein chains

Q8AV11  (Q8AV11_ONCKE) -  Anionic trypsin (Fragment) from Oncorhynchus keta

Seq: 222 a.a.

Struc: 220 a.a.

DOI no: 10.1107/S0907444909012165

Acta Crystallogr D Biol Crystallogr 65:717-723 (2009)

PubMed id: 19564692

A structural comparison of three isoforms of anionic trypsin from chum salmon (Oncorhynchus keta).

E.Toyota, D.Iyaguchi, H.Sekizaki, M.Tateyama, K.K.Ng.

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.

Selected figure(s)

Figure 1.
Figure 1 Superimposition of the C^ atoms in CST-1, CST-2 and CST-3. The C^ traces of CST-1, CST-2 and CST-3 are shown in blue, green and red, respectively. The three catalytic residues (Asp102, His57 and Ser195), benzamidine and calcium ions are included. The autolysis loop is shown as a red dashed circle.

Figure 3.
Figure 3 A comparison of the interactions of the C-terminal -helix with the N-terminal domain between the three isozymes. The interactions of the extremity of the C-terminal -helix with the N-terminal domain are shown for CST-1 (a), CST-2 (b) and CST-3 (c). The red dashed lines indicate hydrogen bonds. Residue numbers are labelled.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2009, 65, 717-723) copyright 2009.

Figures were selected by an automated process.