1T7C

CRYSTAL STRUCTURE OF THE P1 GLU BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of five bovine chymotrypsin complexes with P1 BPTI variants.

Czapinska, H.Helland, R.Smalas, A.O.Otlewski, J.

(2004) J.Mol.Biol. 344: 1005-1020

  • DOI: 10.1016/j.jmb.2004.09.088
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bovine chymotrypsin-bovine pancreatic trypsin inhibitor (BPTI) interaction belongs to extensively studied models of protein-protein recognition. The accommodation of the inhibitor P1 residue in the S1 binding site of the enzyme forms the hot spot ...

    The bovine chymotrypsin-bovine pancreatic trypsin inhibitor (BPTI) interaction belongs to extensively studied models of protein-protein recognition. The accommodation of the inhibitor P1 residue in the S1 binding site of the enzyme forms the hot spot of this interaction. Mutations introduced at the P1 position of BPTI result in a more than five orders of magnitude difference of the association constant values with the protease. To elucidate the structural aspects of the discrimination between different P1 residues, crystal structures of five bovine chymotrypsin-P1 BPTI variant complexes have been determined at pH 7.8 to a resolution below 2 A. The set includes polar (Thr), ionizable (Glu, His), medium-sized aliphatic (Met) and large aromatic (Trp) P1 residues and complements our earlier studies of the interaction of different P1 side-chains with the S1 pocket of chymotrypsin. The structures have been compared to the complexes of proteases with similar and dissimilar P1 preferences, including Streptomyces griseus proteases B and E, human neutrophil elastase, crab collagenase, bovine trypsin and human thrombin. The S1 sites of these enzymes share a common general shape of significant rigidity. Large and branched P1 residues adapt in their complexes similar conformations regardless of the polarity and size differences between their S1 pockets. Conversely, long and flexible residues such as P1 Met are present in the disordered form and display a conformational diversity despite similar inhibitory properties with respect to most enzymes studied. Thus, the S1 specificity profiles of the serine proteases appear to result from the precise complementarity of the P1-S1 interface and minor conformational adjustments occurring upon the inhibitor binding.


    Related Citations: 
    • Crystal structure of the bovine alpha-chymotrypsin:Kunitz inhibitor complex. An example of multiple protein:protein recognition sites.
      Capasso, C.,Rizzi, M.,Menegatti, E.,Ascenzi, P.,Bolognesi, M.
      (1997) J.Mol.Recog. 10: 26
    • CRYSTALLOGRAPHIC REFINEMENT OF THE STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR AT 1.5 A RESOLUTION
      DEISENHOFER, J.,STEIGEMANN, W.
      (1975) Acta Crystallogr.,Sect.B 31: 238
    • Three-dimensional structure of tosyl-alpha-chymotrypsin
      Matthews, B.W.,Sigler, P.B.,Henderson, R.,Blow, D.M.
      (1967) Nature 214: 652
    • STRUCTURAL CONSEQUENCES OF ACCOMMODATION OF FOUR NON-COGNATE AMINO-ACID RESIDUES IN THE S1 POCKET OF BOVINE TRYPSIN AND CHYMOTRYPSIN
      HELLAND, R.,CZAPINSKA, H.,LEIROS, I.,OLUFSEN, M.,OTLEWSKI, J.,SMALAS, A.O.
      (2003) J.Mol.Biol. 333: 845
    • Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities
      Scheidig, A.J.,Hynes, T.R.,Pelletier, L.A.,Wells, J.A.,Kossiakoff, A.A.
      (1997) Protein Sci. 6: 1806
    • ULTRAHIGH-RESOLUTION STRUCTURE OF A BPTI MUTANT
      ADDLAGATTA, A.,CZAPINSKA, H.,KRZYWDA, S.,OTLEWSKI, J.,JASKOLSKI, M.
      (2001) Acta Crystallogr.,Sect.D 57: 649


    Organizational Affiliation

    Laboratory of Protein Engineering, Institute of Biochemistry and Molecular Biology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chymotrypsin A
A, C
245Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pancreatic trypsin inhibitor
B, D
58Bos taurusMutation(s): 2 
Find proteins for P00974 (Bos taurus)
Go to UniProtKB:  P00974
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 99.980α = 90.00
b = 99.980β = 90.00
c = 205.370γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4data scaling
CNSphasing
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance