1DS3

CRYSTAL STRUCTURE OF OMTKY3-CH2-ASP19I

Summary for 1DS3

• Entry DOI: 10.2210/pdb1ds3/pdb
• Related: 1SGP 1SGQ 1SGR 2SGP 3SGP
• Descriptor: OVOMUCOID (2 entities in total)
• Functional Keywords: canonical protein inhibitor, ovomucoid, reduced peptide bond, omtky3, hydrolase inhibitor
• Biological source: Meleagris gallopavo (turkey)
• Cellular location: Secreted: P68390
• Total number of polymer chains: 1
• Total formula weight: 5557.28

Authors

Bateman, K.S.,Huang, K.,Anderson, S.,Lu, W.,Qasim, M.A.,Laskowski Jr., M.,James, M.N.G. (deposition date: 2000-01-06, release date: 2001-01-31, Last modification date: 2021-11-03)

Primary citation

Bateman, K.S.,Huang, K.,Anderson, S.,Lu, W.,Qasim, M.A.,Laskowski Jr., M.,James, M.N.
Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with Streptomyces griseus proteinase B (SGPB) and the structure of the free inhibitor, OMTKY-3-psi[CH2NH2+]-Asp19I
J.Mol.Biol., 305:839-849, 2001

PubMed Abstract: X-ray crystallography has been used to determine the 3D structures of two complexes between Streptomyces griseus proteinase B (SGPB), a bacterial serine proteinase, and backbone variants of turkey ovomucoid third domain (OMTKY3). The natural P1 residue (Leu18I) has been substituted by a proline residue (OMTKY3-Pro18I) and in the second variant, the peptide bond between Thr17I and Leu18I was replaced by an ester bond (OMTKY3-psi[COO]-Leu18I). Both variants lack the P1 NH group that donates a bifurcated hydrogen bond to the carbonyl O of Ser214 and O(gamma) of the catalytic Ser195, one of the common interactions between serine proteinases and their canonical inhibitors. The SGPB:OMTKY3-Pro18I complex has many structural differences in the vicinity of the S1 pocket when compared with the previously determined structure of SGPB:OMTKY3-Leu18I. The result is a huge difference in the DeltaG degrees of binding (8.3 kcal/mol), only part of which can be attributed to the missing hydrogen bond. In contrast, very little structural difference exists between the complexes of SGPB:OMTKY3-psi[COO]-Leu18I and SGPB:OMTKY3-Leu18I, aside from an ester O replacing the P1 NH group. Therefore, the difference in DeltaG degrees, 1.5 kcal/mol as calculated from the measured equilibrium association constants, can be attributed to the contribution of the P1 NH hydrogen bond toward binding. A crystal structure of OMTKY3 having a reduced peptide bond between P1 Leu18I and P'1 Asp19I, (OMTKY3-psi[CH2NH2+]-Asp19I) has also been determined by X-ray crystallography. This variant has very weak association equilibrium constants with SGPB and with chymotrypsin. The structure of the free inhibitor suggests that the reduced peptide bond has not introduced any major structural changes in the inhibitor. Therefore, its poor ability to inhibit serine proteinases is likely due to the disruptions of the canonical interactions at the oxyanion hole.

PubMed: 11162096
DOI: 10.1006/jmbi.2000.4343

Experimental method

X-RAY DIFFRACTION (1.65 Å)