2GMT

THREE-DIMENSIONAL STRUCTURE OF CHYMOTRYPSIN INACTIVATED WITH (2S) N-ACETYL-L-ALANYL-L-PHENYLALANYL-CHLOROETHYL KETONE: IMPLICATIONS FOR THE MECHANISM OF INACTIVATION OF SERINE PROTEASES BY CHLOROKETONES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structure of chymotrypsin inactivated with (2S)-N-acetyl-L-alanyl-L-phenylalanyl alpha-chloroethane: implications for the mechanism of inactivation of serine proteases by chloroketones.

Kreutter, K.Steinmetz, A.C.Liang, T.C.Prorok, M.Abeles, R.H.Ringe, D.

(1994) Biochemistry 33: 13792-13800

  • DOI: https://doi.org/10.1021/bi00250a033
  • Primary Citation of Related Structures:  
    2GMT

  • PubMed Abstract: 

    The reaction of enantiomerically pure (2S)-N-acetyl-L-alanyl-L-phenylalanyl alpha-chloroethane with gamma-chymotrypsin was studied as a probe of the mechanism of inactivation of serine proteases by peptidyl chloroalkanes. It was determined crystallographically that the peptidyl chloroethane alkylates His57 with retention of configuration at the chiral center, indicating a double displacement mechanism. We think it likely that a Ser195-epoxy ether adduct is an intermediate on the inactivation pathway, although other possibilities have not been disproven. Kinetic data reported by others [Angliker et al. (1988) Biochem. J. 256, 481-486] indicate that the epoxy ether intermediate is not an irreversibly inactivated form of enzyme [a conclusion confirmed experimentally (Prorok et al. (1994) Biochemistry 33, 9784-9790)] and that both ring closure of the tetrahedral intermediate to form the epoxy ether and ring opening by His57 partially limit the first-order rate constant for inactivation, ki. The peptidyl chloroethyl derivative adopts a very different active site conformation from that assumed by serine proteases inactivated by peptidyl chloromethanes. Positioning the chloroethyl derivative into the conformation adopted by chloromethyl derivatives would cause the extra methyl group to make a bad van der Waals contact with the inactivator P2 carbonyl carbon, thereby preventing the formation of the invariant hydrogen bond between the inactivator P1 amide nitrogen and the carbonyl group of Ser214. We conclude that the unusual conformation displayed by the chloroethyl derivative is caused by steric hindrance between the extra methyl group and the rest of the inactivator chain.


  • Organizational Affiliation

    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GAMMA-CHYMOTRYPSIN13Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus)
Explore P00766 
Go to UniProtKB:  P00766
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00766
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GAMMA-CHYMOTRYPSIN131Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus)
Explore P00766 
Go to UniProtKB:  P00766
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00766
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GAMMA-CHYMOTRYPSIN97Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus)
Explore P00766 
Go to UniProtKB:  P00766
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00766
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HIN
Query on HIN

Download Ideal Coordinates CCD File 
D [auth B](2S) N-ACETYL-L-ALANYL-ALPHAL-PHENYLALANYL-CHLOROETHYLKETONE
C16 H21 Cl N2 O3
WABWAIGLGFELMI-FZMZJTMJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.188 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.5α = 90
b = 69.5β = 90
c = 97.6γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other