7TLN

STRUCTURAL ANALYSIS OF THE INHIBITION OF THERMOLYSIN BY AN ACTIVE-SITE-DIRECTED IRREVERSIBLE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of the inhibition of thermolysin by an active-site-directed irreversible inhibitor.

Holmes, M.A.Tronrud, D.E.Matthews, B.W.

(1983) Biochemistry 22: 236-240


  • PubMed Abstract: 
  • The mode of binding of the irreversible thermolysin inhibitor ClCH2CO-DL-(N-OH)Leu-OCH3 [Rasnick, D., & Powers, J.C. (1978) Biochemistry 17, 4363-4369] has been determined by X-ray crystallography at a resolution of 2.3 A and the structure of the cov ...

    The mode of binding of the irreversible thermolysin inhibitor ClCH2CO-DL-(N-OH)Leu-OCH3 [Rasnick, D., & Powers, J.C. (1978) Biochemistry 17, 4363-4369] has been determined by X-ray crystallography at a resolution of 2.3 A and the structure of the covalent complex refined to give a crystallographic residual of 17.0%. This is the first such structural study of an active-site-directed covalent complex of a zinc protease. As anticipated by Rasnick and Powers, the inhibitor alkylates Glu-143 in the thermolysin active site, and the hydroxamic acid moiety coordinates the zinc ion. The formation of the covalent complex is associated with a significant shift in a segment of the polypeptide backbone in the vicinity of the active site. This conformational adjustment appears to be necessary to relieve steric hindrance which would otherwise prevent alkylation of Glu-143. It is suggested that this steric hindrance, which occurs for thermolysin but would not be expected for carboxypeptidase A, accounts for the previously inexplicable difference in reactivity of these two metalloproteases toward N-haloacetyl amino acids. The relevance of this steric hindrance to the mechanism of catalysis is discussed. In agreement with previous results [Kester, W. R., & Matthews, B. W. (1977) Biochemistry 16, 2506-2516], it appears that steric hindrance prevents the direct attack of Glu-143 on the carbonyl carbon of an extended substrate, therefore ruling out the anhydride pathway in thermolysin-catalyzed hydrolysis of polypeptide substrates and their ester analogues.


    Related Citations: 
    • Binding of the Biproduct Analog L-Benzylsuccinic Acid to Thermolysin Determined by X-Ray Crystallography
      Bolognesi, M.C.,Matthews, B.W.
      (1979) J.Biol.Chem. 254: 634
    • Structure of Thermolysin Refined at 1.6 Angstroms Resolution
      Holmes, M.A.,Matthews, B.W.
      (1982) J.Mol.Biol. 160: 623
    • Role of Calcium in the Thermal Stability of Thermolysin
      Dahlquist, F.W.,Long, J.W.,Bigbee, W.L.
      (1976) Biochemistry 15: 1103
    • Amino-Acid Sequence of Thermolysin
      Titani, K.,Hermodson, M.A.,Ericsson, L.H.,Walsh, K.A.,Neurath, H.
      (1972) Nature New Biol. 238: 35
    • Comparison of the Structures of Carboxypeptidase a and Thermolysin
      Kester, W.R.,Matthews, B.W.
      (1977) J.Biol.Chem. 252: 7704
    • Evidence of Homologous Relationship between Thermolysin and Neutral Protease a of Bacillus Subtilis
      Levy, P.L.,Pangburn, M.K.,Burstein, Y.,Ericsson, L.H.,Neurath, H.,Walsh, K.A.
      (1975) Proc.Natl.Acad.Sci.USA 72: 4341
    • The Conformation of Thermolysin
      Matthews, B.W.,Weaver, L.H.,Kester, W.R.
      (1974) J.Biol.Chem. 249: 8030
    • Crystallographic Study of the Binding of Dipeptide Inhibitors to Thermolysin. Implications for the Mechanism of Catalysis
      Kester, W.R.,Matthews, B.W.
      (1977) Biochemistry 16: 2506
    • Structure of Thermolysin
      Matthews, B.W.,Colman, P.M.,Jansonius, J.N.,Titani, K.,Walsh, K.A.,Neurath, H.
      (1972) Nature New Biol. 238: 41
    • Three Dimensional Structure of Thermolysin
      Matthews, B.W.,Jansonius, J.N.,Colman, P.M.,Schoenborn, B.P.,Duporque, D.
      (1972) Nature New Biol. 238: 37
    • A Crystallographic Study of the Complex of Phosphoramidon with Thermolysin. A Model for the Presumed Catalytic Transition State and for the Binding of Extended Substrates
      Weaver, L.H.,Kester, W.R.,Matthews, B.W.
      (1977) J.Mol.Biol. 114: 119
    • Structure of a Mercaptan-Thermolysin Complex Illustrates Mode of Inhibition of Zinc Proteases by Substrate-Analogue Mercaptans
      Monzingo, A.F.,Matthews, B.W.
      (1982) Biochemistry 21: 3390
    • The Structure of Thermolysin,an Electron Density Map at 2.3 Angstroms Resolution
      Colman, P.M.,Jansonius, J.N.,Matthews, B.W.
      (1972) J.Mol.Biol. 70: 701
    • Binding of Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis
      Holmes, M.A.,Matthews, B.W.
      (1981) Biochemistry 20: 6912
    • Binding of Lanthanide Ions to Thermolysin
      Matthews, B.W.,Weaver, L.H.
      (1974) Biochemistry 13: 1719



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMOLYSIN
A
316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
INC
Query on INC

Download SDF File 
Download CCD File 
A
2-(ACETYL-HYDROXY-AMINO)-4-METHYL-PENTANOIC ACID METHYL ESTER
C9 H17 N O4
OVUHENJPIUQHLJ-MRVPVSSYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.170 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.200α = 90.00
b = 94.200β = 90.00
c = 131.400γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1983-03-09
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other