1D6R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.

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

(2000) J.Mol.Biol. 298: 477-491

  • DOI: 10.1006/jmbi.2000.3677

  • PubMed 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 wi ...

    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.


    Related Citations: 
    • Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28-nm resolution-structural peculiarities in a folded protein conformation.
      Voss, R.H.,Ermler, U.,Essen, L.O.,Wenzl, G.,Kim, Y.M.,Flecker, P.
      (1996) Eur.J.Biochem. 242: 122
    • Mutational analysis of disulfide bonds in the trypsin-reactive subdomain of a Bowman-Birk-type inhibitor of trypsin and chymotrypsin. Cooperative versus autonomous refolding of subdomains.
      Philipp, S.,Kim, Y.M.,Durr, I.,Wenzl, G.,Vogt, M.,Flecker, P.
      (1998) Eur.J.Biochem. 251: 854
    • Proteolytic cleavage of soybean Bowman-Birk inhibitor monitored by means of high-performance capillary electrophoresis
      Jensen, B.,Unger, K.K.,Uebe, J.,Gey, M.,Kim, Y.M.,Flecker, P.
      (1996) J.Biochem.Biophys.Methods 33: 171
    • Chemical synthesis, molecular cloning and expression of gene coding for a Bowman-Birk-type proteinase inhibitor
      Flecker, P.
      (1987) Eur.J.Biochem. 166: 151
    • Template-directed protein folding into a metastable state of increased activity
      Flecker, P.
      (1995) Eur.J.Biochem. 232: 528
    • A new and general procedure for refolding mutant Bowman-Birk-type proteinase inhibitors on trypsin-Sepharose as a matrix with complementary structure
      Flecker, P.
      (1989) FEBS Lett. 252: 153


    Organizational Affiliation

    Max Planck Institut für Biophysik, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSINOGEN
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BOWMAN-BIRK PROTEINASE INHIBITOR PRECURSOR
I
58Glycine maxMutation(s): 0 
Find proteins for P01055 (Glycine max)
Go to UniProtKB:  P01055
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.152 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.600α = 90.00
b = 55.600β = 90.00
c = 183.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
ROTAVATAdata reduction
ROTAVATAdata scaling
WEISdata scaling
CCP4data scaling
WEISdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description