PDBsum entry 1ab9

Complex (serine protease/peptide)

PDB id: 1ab9

Contents

Protein chains

131 a.a. *

96 a.a. *

Ligands

CYS-GLY-VAL-PRO-ALA-ILE-GLN-PRO-VAL-LEU

THR-PRO-GLY-VAL-TYR

SO4

Waters ×127

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: X-Ray crystal structure of a dipeptide-Chymotrypsin complex in an inhibitory interaction.
• Authors: A.Kashima, Y.Inoue, S.Sugio, I.Maeda, T.Nose, Y.Shimohigashi.
• Ref.: Eur J Biochem, 1998, 255, 12-23.
• PubMed id: 9692896

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.

Secondary reference #1

• Title: Gamma-Chymotrypsin is a complex of alpha-Chymotrypsin with its own autolysis products.
• Authors: M.Harel, C.T.Su, F.Frolow, I.Silman, J.L.Sussman.
• Ref.: Biochemistry, 1991, 30, 5217-5225. [DOI no: 10.1021/bi00235a015]
• PubMed id: 2036388

Secondary reference #2

• Title: 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.
• Authors: M.M.Dixon, R.G.Brennan, B.W.Matthews.
• Ref.: Int J Biol Macromol, 1991, 13, 89-96. [DOI no: 10.1016/0141-8130(91)90054-X]
• PubMed id: 1888717

Secondary reference #3

• Title: Is gamma-Chymotrypsin a tetrapeptide acyl-Enzyme adduct of alpha-Chymotrypsin?
• Authors: M.M.Dixon, B.W.Matthews.
• Ref.: Biochemistry, 1989, 28, 7033-7038. [DOI no: 10.1021/bi00443a038]
• PubMed id: 2819046