1AFQ

CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED WITH A SYNTHETIC INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction.

Kashima, A.Inoue, Y.Sugio, S.Maeda, I.Nose, T.Shimohigashi, Y.

(1998) Eur.J.Biochem. 255: 12-23

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The dipeptide D-leucyl-L-phenylalanyl p-fluorobenzylamide (D-Leu-Phe-NH-BzlF) inhibits chymotrypsin strongly in a competitive manner with the Ki value of 0.61 microM [Shimohigashi, Y., Maeda, I., Nose, T., Ikesue, K., Sakamoto, H., Ogawa, T., Ide, Y. ...

    The dipeptide D-leucyl-L-phenylalanyl p-fluorobenzylamide (D-Leu-Phe-NH-BzlF) inhibits chymotrypsin strongly in a competitive manner with the Ki value of 0.61 microM [Shimohigashi, Y., Maeda, I., Nose, T., Ikesue, K., Sakamoto, H., Ogawa, T., Ide, Y., Kawahara, M., Nezu, T., Terada, Y., Kawano, K. & Ohno, M. (1996) J. Chem. Soc. Perkin Trans. 1, 2479-2485]. The structure/activity studies have suggested a unique inhibitory conformation, in which the C-terminal benzyl group fits the chymotrypsin S1 site and the hydrophobic core constructed by the side chains of D-Leu-Phe fits the S2 or S1' site. To verify this assumption, the molecular structure of the complex between the dipeptide and gamma-chymotrypsin has been determined crystallographically. Gamma-chymotrypsin itself was first crystallized and refined at 1.6-A resolution. The refined structure was virtually identical to the conformation reported and the electron density at the active site was interpreted as a pentapeptide Thr-Pro-Gly-Val-Tyr derived from autolysis of the enzyme (residues 224-228). The chymotrypsin-dipeptide complex was obtained by soaking the crystals of gamma-chymotrypsin in a solution saturated with the dipeptide inhibitor. The crystal structure of the complex has been refined at 1.8-A resolution to a crystallographic R-factor of 18.1%. The structure of gamma-chymotrypsin in the complex agreed fairly well with that of gamma-chymotrypsin per se with a rmsd of 0.13 A for all the C alpha carbons. Two inhibitor molecules were assigned in an asymmetric unit, i.e. one in the active site and the other at the interface of two symmetry-related enzyme molecules. In both sites dipeptides adopted very similar folded conformations, in which side chains of D-Leu-Phe are spatially proximal. In the active site where the binding of dipeptide was judged to be a direct cause of inhibition, C-terminal p-fluorobenzylamide group of the dipeptide, NH-BzlF, was found in the S1 hydrophobic pocket. At the bottom of this pocket, the p-fluorine atom hydrogen bonded with a water molecule, probably to enhance the inhibitory activity. The stereospecific interaction of R and S isomers of the dipeptide with C-terminal NH-C*H(CH3)-C6H5 was well explained by the space available for methyl replacement in the complex. The hydrophobic core constructed by side chains of D-Leu-Phe was found at the broad S2 site. Interestingly, a novel interaction was found between the inhibitor Phe residue and chymotrypsin His57, the phenyl of Phe and the imidazole of His being in a pi-pi stacking interaction at a distance 3.75 A.


    Related Citations: 
    • Structure of Gamma-Chymotrypsin in the Range Ph 2.0 To Ph 10.5 Suggests that Gamma-Chymotrypsin is a Covalent Acyl-Enzyme Adduct at Low Ph
      Dixon, M.M.,Brennan, R.G.,Matthews, B.W.
      (1991) Int.J.Biol.Macromol. 13: 89
    • Gamma-Chymotrypsin is a Complex of Alpha-Chymotrypsin with its Own Autolysis Products
      Harel, M.,Su, C.-T.,Frolow, F.,Silman, I.,Sussman, J.L.
      (1991) Biochemistry 30: 5217
    • Is Gamma-Chymotrypsin a Tetrapeptide Acyl-Enzyme Adduct of Alpha-Chymotrypsin?
      Dixon, M.M.,Matthews, B.W.
      (1989) Biochemistry 28: 7033


    Organizational Affiliation

    Research Division, The Green Cross Corp., Hirakata, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BOVINE GAMMA-CHYMOTRYPSIN
A
13Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BOVINE GAMMA-CHYMOTRYPSIN
B
131Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BOVINE GAMMA-CHYMOTRYPSIN
C
96Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
0FG
Query on 0FG

Download SDF File 
Download CCD File 
B, C
D-leucyl-N-(4-fluorobenzyl)-L-phenylalaninamide
C22 H28 F N3 O2
BCQKEAUFNXECKN-UXHICEINSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000279 (0FG)
Query on PRD_000279
B,CD-LEUCYL-L-PHENYLALANYL-P-FLUOROBENZYLAMIDEPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.181 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.840α = 90.00
b = 69.840β = 90.00
c = 97.360γ = 90.00
Software Package:
Software NamePurpose
CONTROLdata reduction
X-PLORrefinement
PROCESSdata scaling
CONTROLdata collection
X-PLORmodel building
PROCESSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-04
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other