1VGC

GAMMA-CHYMOTRYPSIN L-PARA-CHLORO-1-ACETAMIDO BORONIC ACID INHIBITOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes.

Stoll, V.S.Eger, B.T.Hynes, R.C.Martichonok, V.Jones, J.B.Pai, E.F.

(1998) Biochemistry 37: 451-462

  • DOI: 10.1021/bi971166o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In order to probe the structural basis of stereoselectivity in the serine protease family, a series of enantiomeric boronic acids RCH2CH(NHCOCH3)B(OH)2 has been synthesized and kinetically characterized as transition-state analog inhibitors using alp ...

    In order to probe the structural basis of stereoselectivity in the serine protease family, a series of enantiomeric boronic acids RCH2CH(NHCOCH3)B(OH)2 has been synthesized and kinetically characterized as transition-state analog inhibitors using alpha-chymotrypsin and subtilisin Carlsberg as model systems. When the R-substituent in this series was changed from a p-chlorophenyl to a 1-naphthyl group, alpha-chymotrypsin, but not subtilisin, reversed its usual preference for l-enantiomers and bound more tightly to the D-enantiomer [Martichonok, V., & Jones, J. B. (1996) J. Am. Chem. Soc. 118, 950-958]. The structural factors responsible for the differences in stereoselectivity between the two enzymes have been explored by X-ray crystallographic examination of subtilisin Carlsberg and gamma-chymotrypsin complexes of the L- and D-enantiomers of p-chlorophenyl and 1-naphthyl boronic acid derivatives. In both enzymes, the L-isomers of the inhibitors, which are more closely related to the natural L-amino acid substrates, form tetrahedral adducts, covalently linking the central boron atom and Ogamma of the catalytic serine. The d-isomers, however, differ in the way they interact with subtilisin or gamma-chymotrypsin. With subtilisin, both the D-p-chlorophenyl and D-1-naphthyl inhibitor complexes form covalent Ser Ogamma-to-boron bonds, but with gamma-chymotrypsin, the same inhibitors lead to novel tetrahedral adducts covalently linking both Ser195 Ogamma and His57 Nepsilon2 covalently via the boron atom.


    Related Citations: 
    • Structure and Activity of Two Photoreversible Cinnamates Bound to Chymotrypsin
      Stoddard, B.L.,Bruhnke, J.,Porter, N.,Ringe, D.,Petsko, G.A.
      (1990) Biochemistry 29: 4871
    • Probing the Specificity of the S1 Binding Site of Subtilisin Carlsberg with Boronic Acids
      Seufer-Wasserthal, P.,Martichonok, V.,Keller, T.H.,Chin, B.,Martin, R.,Jones, J.B.
      (1994) Bioorg.Med.Chem. 2: 35
    • Gamma-Chymotrypsin is a Complex of Alpha-Chymotrypsin with its Own Autolysis Products
      Harel, M.,Su, C.T.,Frolow, F.,Silman, I.,Sussman, J.L.
      (1991) Biochemistry 30: 5217
    • Probing the Specificity of the Serine Proteases Subtilisin Carlsberg and A-Chymotrypsin with Enantiomeric 1-Acetamido Boronic Acids. An Unexpected Reversal of the Normal
      Martichonok, V.,Jones, J.B.
      (1996) J.Am.Chem.Soc. 118: 95


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GAMMA CHYMOTRYPSIN
A
13Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GAMMA CHYMOTRYPSIN
B
131Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GAMMA CHYMOTRYPSIN
C
97Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
V36
Query on V36

Download SDF File 
Download CCD File 
C
L-1-(4-CHLOROPHENYL)-2-(ACETAMIDO)ETHANE BORONIC ACID
L-PARA-CHLORO-1-ACETAMIDO BORONIC ACID
C10 H14 B Cl N O4
FPCXTDQHLFRWCJ-JTQLQIEISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V36Ki: 1200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.860α = 90.00
b = 69.860β = 90.00
c = 97.150γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance