PDBsum entry 1d6r

Hydrolase

PDB id: 1d6r

Contents

Protein chains

223 a.a. *

58 a.a. *

Waters ×116

* Residue conservation analysis

PDB id:

1d6r

Name:

Hydrolase

Title:

Crystal structure of cancer chemopreventive bowman-birk inhibitor in ternary complex with bovine trypsin at 2.3 a resolution. Structural basis of janus-faced serine protease inhibitor specificity

Structure:

Trypsinogen. Chain: a. Fragment: cationic precursor. Bowman-birk proteinase inhibitor precursor. Chain: i

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Cell: acinar cell. Glycine max. Soybean. Organism_taxid: 3847

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.30Å R-factor: 0.152 R-free: 0.226

Authors:

J.Koepke,U.Ermler,G.Wenzl,P.Flecker

Key ref:

J.Koepke et al. (2000). Crystal structure of cancer chemopreventive Bowman-Birk inhibitor in ternary complex with bovine trypsin at 2.3 A resolution. Structural basis of Janus-faced serine protease inhibitor specificity. J Mol Biol, 298, 477-491. PubMed id: 10772864 DOI: 10.1006/jmbi.2000.3677

Date:

15-Oct-99 Release date: 05-May-00

Protein chain

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.

Protein chain

P01055  (IBB1_SOYBN) -  Bowman-Birk type proteinase inhibitor from Glycine max

Seq: 110 a.a.

Struc: 58 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1006/jmbi.2000.3677

J Mol Biol 298:477-491 (2000)

PubMed id: 10772864

Crystal structure of cancer chemopreventive Bowman-Birk inhibitor in ternary complex with bovine trypsin at 2.3 A resolution. Structural basis of Janus-faced serine protease inhibitor specificity.

J.Koepke, U.Ermler, E.Warkentin, G.Wenzl, P.Flecker.

ABSTRACT

Understanding molecular recognition on a structural basis is an objective with broad academic and applied significance. In the complexes of serine proteases and their proteinaceous inhibitors, recognition is governed mainly by residue P1 in accord with primary serine protease specificity. The bifunctional soybean Bowman-Birk inhibitor (sBBI) should, therefore, interact at LysI16 (subdomain 1) with trypsin and at LeuI43 (subdomain 2) with chymotrypsin. In contrast with this prediction, a 2:1 assembly with trypsin was observed in solution and in the crystal structure of sBBI in complex with trypsin, determined at 2.3 A resolution by molecular replacement. Strikingly, P1LeuI43 of sBBI was fully embedded into the S(1) pocket of trypsin in contrast to primary specificity. The triple-stranded beta-hairpin unique to the BBI-family and the surface loops surrounding the active site of the enzyme formed a protein-protein-interface far extended beyond the primary contact region. Polar residues, hydrophilic bridges and weak hydrophobic contacts were predominant in subdomain 1, interacting specifically with trypsin. However, close hydrophobic contacts across the interface were characteristic of subdomain 2 reacting with both trypsin and chymotrypsin. A Met27Ile replacement shifted the ratio with trypsin to the predicted 1:1 ratio. Thus, the buried salt-bridge responsible for trypsin specificity was stabilised in a polar, and destabilized in a hydrophobic, environment. This may be used for adjusting the specificity of protease inhibitors for applications such as insecticides and cancer chemopreventive agents.

Selected figure(s)

Figure 1.
Figure 1. Schematic representation of active site of bovine trypsin. The catalytic triad Ser195, His57 and Asp102 of the enzyme are shown in the centre. The NH group atoms of Ser195 and Gly193 forming the oxyanion hole were omitted for clarity. The walls 189-195, 214-220 and 225-228 and the surface loops 185-188 and 221-225 of the S1 pocket are highlighted in blue and in green-blue. The surface loops 90-104 (magenta), 140-156 (red) and 171-178 (violet) surrounding the S1 pocket are also highlighted. Residues 15-19 of sBBI are shown in orange. The side-chains of Leu99, Trp215 and Tyr172 forming the S4 pocket and those of Tyr151 and Gln192 (deleted beyond C^b forming the S2' pocket are shown. The side-chain of P1LysI16 interacting with Asp189 is shown. Amino acid side-chains are numbered near the C^a atoms, but in Asp189, Tyr151, Tyr172 and Trp215 they are numbered at their tips.

Figure 6.
Figure 6. Buried surface area. The buried surface area was viewed along the crystallographic 2-fold axis with subdomain 1 on the left and subdomain 2 on the right. Red, polar residues; green, hydrophobic residues. The two trypsin molecules are indicated by yellow lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 477-491) copyright 2000.

Figures were selected by an automated process.