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PDBsum entry 1afq

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protein ligands Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
1afq
Jmol
Contents
Protein chains
131 a.a. *
96 a.a. *
Ligands
CYS-GLY-VAL-PRO-
ALA-ILE-GLN-PRO-
VAL-LEU
0FG ×2
SO4
Waters ×127
* Residue conservation analysis
PDB id:
1afq
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure of bovine gamma-chymotrypsin complexed wit synthetic inhibitor
Structure: Bovine gamma-chymotrypsin. Chain: a. Bovine gamma-chymotrypsin. Chain: b. Bovine gamma-chymotrypsin. Chain: c. Ec: 3.4.21.1
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Organ: pancreas
Biol. unit: Trimer (from PQS)
Resolution:
1.80Å     R-factor:   0.181     R-free:   0.182
Authors: S.Sugio,A.Kashima,Y.Inoue,I.Maeda,T.Nose,Y.Shimohigashi
Key ref: A.Kashima et al. (1998). X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction. Eur J Biochem, 255, 12-23. PubMed id: 9692896
Date:
12-Mar-97     Release date:   17-Sep-97    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
Seq:
Struc:
245 a.a.
131 a.a.
Protein chain
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
Seq:
Struc:
245 a.a.
96 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains B, C: E.C.3.4.21.1  - Chymotrypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Tyr-|-Xaa, Trp-|-Xaa, Phe-|-Xaa, Leu-|-Xaa.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
Eur J Biochem 255:12-23 (1998)
PubMed id: 9692896  
 
 
X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction.
A.Kashima, Y.Inoue, S.Sugio, I.Maeda, T.Nose, Y.Shimohigashi.
 
  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., 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17279501 H.Yuki, Y.Tanaka, M.Hata, H.Ishikawa, S.Neya, and T.Hoshino (2007).
Implementation of pi-pi interactions in molecular dynamics simulation.
  J Comput Chem, 28, 1091-1099.  
15731882 R.Smoum, A.Rubinstein, and M.Srebnik (2005).
Noncovalent inhibition of the serine proteases, alpha-chymotrypsin and trypsin by trifluoro(organo)borates.
  Org Biomol Chem, 3, 941-944.  
15122639 J.A.Olsen, D.W.Banner, P.Seiler, B.Wagner, T.Tschopp, U.Obst-Sander, M.Kansy, K.Müller, and F.Diederich (2004).
Fluorine interactions at the thrombin active site: protein backbone fragments H-C(alpha)-C=O comprise a favorable C-F environment and interactions of C-F with electrophiles.
  Chembiochem, 5, 666-675.  
10944388 V.Z.Pletnev, T.S.Zamolodchikova, W.A.Pangborn, and W.L.Duax (2000).
Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities.
  Proteins, 41, 8.
PDB code: 1euf
10380349 Y.Shimohigashi, T.Nose, Y.Yamauchi, and I.Maeda (1999).
Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/pie interaction.
  Biopolymers, 51, 9.  
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