1ab9
From Proteopedia
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CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN
Overview
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.
About this Structure
1AB9 is a Protein complex structure of sequences from Bos taurus with SO4 as ligand. Active as Chymotrypsin, with EC number 3.4.21.1 Known structural/functional Site: . Full crystallographic information is available from OCA.
Reference
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, Eur J Biochem. 1998 Jul 1;255(1):12-23. PMID:9692896
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