1DS2

CRYSTAL STRUCTURE OF SGPB:OMTKY3-COO-LEU18I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Bateman, K.S.Huang, K.Anderson, S.Lu, W.Qasim, M.A.Laskowski Jr., M.James, M.N.

(2001) J.Mol.Biol. 305: 839-849

  • DOI: 10.1006/jmbi.2000.4343
  • Primary Citation of Related Structures:  1DS3, 2SGP

  • 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 resid ...

    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.


    Organizational Affiliation

    Medical Research Council of Canada Group in Protein Structure and Function Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEINASE B (SGPB)
E
185Streptomyces griseusGene Names: sprB
EC: 3.4.21.81
Find proteins for P00777 (Streptomyces griseus)
Go to UniProtKB:  P00777
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
OVOMUCOID
I
51Meleagris gallopavoN/A
Find proteins for P68390 (Meleagris gallopavo)
Go to UniProtKB:  P68390
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
1LU
Query on 1LU
I
non-polymerC6 H12 O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.413α = 90.00
b = 54.647β = 119.13
c = 45.525γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building
XPRESSdata collection
XPRESSdata reduction
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance