PDBsum entry 3bg4

Hydrolase/hydrolase inhibitor

PDB id: 3bg4

Contents

Protein chains

11 a.a.

131 a.a. *

97 a.a. *

46 a.a. *

Waters ×82

* Residue conservation analysis

PDB id:

3bg4

Name:

Hydrolase/hydrolase inhibitor

Title:

The crystal structure of guamerin in complex with chymotrypsin and the development of an elastase-specific inhibitor

Structure:

Chymotrypsin a chain a. Chain: a. Chymotrypsin a chain b. Chain: b. Chymotrypsin a chain c. Chain: c. Guamerin. Chain: d. Engineered: yes

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Hirudo nipponia. Leech. Organism_taxid: 42736. Expressed in: pichia pastoris. Expression_system_taxid: 4922

Resolution:

2.50Å R-factor: 0.187 R-free: 0.241

Authors:

H.Kim,T.T.T.Chu,D.Y.Kim,D.R.Kim,C.M.T.Nguyen,J.Choi,J.R.Lee,M.J.Hahn, K.K.Kim

Key ref:

H.Kim et al. (2008). The crystal structure of guamerin in complex with chymotrypsin and the development of an elastase-specific inhibitor. J Mol Biol, 376, 184-192. PubMed id: 18155725 DOI: 10.1016/j.jmb.2007.11.089

Date:

26-Nov-07 Release date: 29-Jul-08

Protein chain

P00767  (CTRB_BOVIN) -  Chymotrypsinogen B from Bos taurus

Seq: 245 a.a.

Struc: 11 a.a.

Protein chain

P00766  (CTRA_BOVIN) -  Chymotrypsinogen A from Bos taurus

Seq: 245 a.a.

Struc: 131 a.a.

Protein chain

P00766  (CTRA_BOVIN) -  Chymotrypsinogen A from Bos taurus

Seq: 245 a.a.

Struc: 97 a.a.

Protein chain

P46443  (GUAM_HIRNI) -  Guamerin from Hirudo nipponia

Seq: 57 a.a.

Struc: 46 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.3.4.21.1 - chymotrypsin.
• Reaction: Preferential cleavage: Tyr-|-Xaa, Trp-|-Xaa, Phe-|-Xaa, Leu-|-Xaa.

DOI no: 10.1016/j.jmb.2007.11.089

J Mol Biol 376:184-192 (2008)

PubMed id: 18155725

The crystal structure of guamerin in complex with chymotrypsin and the development of an elastase-specific inhibitor.

H.Kim, T.T.Chu, D.Y.Kim, D.R.Kim, C.M.Nguyen, J.Choi, J.R.Lee, M.J.Hahn, K.K.Kim.

ABSTRACT

Guamerin, a canonical serine protease inhibitor from Hirudo nipponia, was identified as an elastase-specific inhibitor and has potential application in various diseases caused by elevated elastase concentration. However, the application of guamerin is limited because it also shows inhibitory activity against other proteases. To improve the selectivity of guamerin as an elastase inhibitor, it is essential to understand the binding mode of the inhibitor to elastase and to other proteases. For this purpose, we determined the crystal structure of guamerin in complex with chymotrypsin at 2.5 A resolution. The binding mode of guamerin on elastase was explored from the model structure of guamerin/elastase. Guamerin binds to the hydrophobic pocket of the protease in a substrate-like manner using its binding loop. In order to improve the binding selectivity of guamerin to elastase, several residues in the binding loop were mutated and the inhibitory activities of the mutants against elastase and chymotrypsin were monitored. The substitution of the Met36 residue for Ala in the P1 site increased the inhibitory activity against elastase up to 14-fold, while the same mutant showed 7-fold decreased activity against chymotrypsin compared to the wild-type guamerin. Furthermore, the M36A guamerin mutant more effectively protected endothelial cells against cell damage caused by elastase than the wild-type guamerin.

Selected figure(s)

Figure 3.
Fig. 3. Cross-sectional views of the S1 binding pockets of BPC and PPE. (a) The surface representation of S1 pocket of BPC is overlapped with the stick model of Met (P1 residue) of wild-type guamerin in the crystal structure of guamerin/BPC. (b) The surface representation of the S1 pocket of PPE in the same view as (a) is overlapped with the stick model of Ala (P1 residue) of mutant guamerin in the model structure of guamerin/PPE.

Figure 4.
Fig. 4. Inhibitory activity of wild-type and M36A mutant guamerin against PPE (a) and BPC (b). Compared with wild-type guamerin, the inhibitory activity of M36A mutant guamerin increased 14-fold against PPE (a), while it decreased 7-fold against BPC (b). The activity change following mutagenesis is represented as an arrow.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 376, 184-192) copyright 2008.

Figures were selected by an automated process.