Crystal structure of the Bowman-Birk inhibitor from barley seeds in ternary complex with porcine trypsin

Eun Young Park, Jeom A. Kim, Hyung Wook Kim, Young Sil Kim, Hyun Kyu Song

Research output: Contribution to journalArticlepeer-review

31 Citations (Scopus)


The structure and function of Bowman-Birk inhibitors (BBIs) from dicotyledonous plants such as soybean have been studied extensively. In contrast, relatively little is known about the BBIs from monocotyledonous plants such as barley, which differ from dicot BBIs in size and tertiary structure. The BBI from barley seeds (BBBI) consists of 125 amino acid residues with two separate inhibitory loops. Previously we determined the high-resolution structure of a 16 kDa BBBI in the free state. The BBBI folds into two compact domains (N and C domain) with tertiary structures that are similar to that of the 8 kDa BBI from dicots. Here we report the structure of a 1: 2 complex between BBBI and porcine pancreatic trypsin (PPT) at 2.2 Å resolution. This structure confirms that several regions, including the inhibitory loops in the free BBBI structure, show exceptionally low temperature factors and a distorted conformation due to crystalline packing in the lattice. Extensive analysis of the interaction between BBBI and trypsin, and comparison with other known canonical inhibitor-protease complexes, reveals that the mode of interaction between BBBI and PPT is similar to that of known serine protease inhibitors, as expected; however, several unique features are also identified in the primary binding sites near the inhibitory loops as well as in additional binding sites. The carboxy-terminal tail of the inhibitor extends into the interface between the two trypsin molecules and interacts with both of them simultaneously. The longest distance between the two P1 residues (Arg17 and Arg76) in the complex structure is approximately 34 Å, which is shorter than in the free inhibitor, but it is still possible for BBBI to bind and inhibit two trypsin molecules simultaneously and independently.

Original languageEnglish
Pages (from-to)173-186
Number of pages14
JournalJournal of Molecular Biology
Issue number1
Publication statusPublished - 2004 Oct 8
Externally publishedYes

Bibliographical note

Funding Information:
We thank Professor N. Sakabe, Drs N. Watanabe, Suzuki, and Igarashi for their assistance during synchrotron data collection at beamline BL-6A of the Photon Factory, Japan. We also thank Professor S. W. Suh for his generous support in the initial stage of this project. This work was supported by a grant from the National Cancer Center (no. 0310130-2 to H.K.S.).


  • anticarcinogenic activity
  • double-headed inhibitor
  • gene duplication
  • inhibitory loop
  • monocotyledonous plant

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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