1TMN

Binding of n-carboxymethyl dipeptide inhibitors to thermolysin determined by x-ray crystallography. a novel class of transition-state analogues for zinc peptidases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Binding of N-carboxymethyl dipeptide inhibitors to thermolysin determined by X-ray crystallography: a novel class of transition-state analogues for zinc peptidases

Monzingo, A.F.Matthews, B.W.

(1984) Biochemistry 23: 5724-5729


  • PubMed Abstract: 
  • The mode of binding of the specific thermolysin inhibitor N-(1-carboxy-3-phenylpropyl)-L-leucyl-L-tryptophan (KI approximately 5 X 10(-8) M) [Maycock, A. L., DeSousa, D. M., Payne, L. G., ten Broeke, J., Wu, M. T., & Patchett, A. A. (1981) Biochem. B ...

    The mode of binding of the specific thermolysin inhibitor N-(1-carboxy-3-phenylpropyl)-L-leucyl-L-tryptophan (KI approximately 5 X 10(-8) M) [Maycock, A. L., DeSousa, D. M., Payne, L. G., ten Broeke, J., Wu, M. T., & Patchett, A. A. (1981) Biochem. Biophys. Res. Commun. 102, 963-969] has been determined by X-ray crystallography and refined to an R value of 17.1% at 1.9-A resolution. The inhibitor binds to thermolysin with both oxygens of the N-carboxymethyl group liganded to the zinc to give overall pentacoordination of the metal. The bidentate ligation of the inhibitor differs from the monodentate binding seen previously for carboxylate-zinc interactions in thermolysin and is closer to the bidentate geometry observed for the binding of hydroxamates [Holmes, M. A., & Matthews, B. W. (1981) Biochemistry 20, 6912-6920]. The geometry of the inhibitor and its interactions with the protein have a number of elements in common with the presumed transition state formed during peptide hydrolysis. The observed zinc ligation supports the previous suggestion that a pentacoordinate intermediate participates in the mechanism of catalysis. However, the alpha-amino nitrogen of the inhibitor is close to Glu-143, suggesting that this residue might accept a proton from an attacking water molecule (as proposed before) and subsequently donate this proton to the leaving nitrogen. By analogy with thermolysin, it is proposed that a related mechanism should be considered for peptide cleavage by carboxypeptidase A.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • 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
    • 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 Gamma Turn. Evidence for a New Folded Conformation in Proteins
      Matthews, B.W.
      (1972) Macromolecules 5: 818
    • 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
    • Structures of Two Thermolysin-Inhibitor Complexes that Differ by a Single Hydrogen Bond
      Tronrud, D.E.,Holden, H.M.,Matthews, B.W.
      (1987) Science 235: 571
    • 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
    • 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
    • The Conformation of Thermolysin
      Matthews, B.W.,Weaver, L.H.,Kester, W.R.
      (1974) J.Biol.Chem. 249: 8030
    • Binding of Lanthanide Ions to Thermolysin
      Matthews, B.W.,Weaver, L.H.
      (1974) Biochemistry 13: 1719
    • 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
    • An Interactive Computer Graphics Study of Thermolysin-Catalyzed Peptide Cleavage and Inhibition by N-Carboxymethyl Dipeptides
      Hangauer, D.G.,Monzingo, A.F.,Matthews, B.W.
      (1984) Biochemistry 23: 5730
    • Amino-Acid Sequence of Thermolysin
      Titani, K.,Hermodson, M.A.,Ericsson, L.H.,Walsh, K.A.,Neurath, H.
      (1972) Nature New Biol. 238: 35
    • The Structure and Stability of Thermolysin
      Weaver, L.H.,Kester, W.R.,Teneyck, L.F.,Matthews, B.W.
      (1976) Experientia,Suppl. 26: 31
    • Rare Earths as Isomorphous Calcium Replacements for Protein Crystallography
      Colman, P.M.,Weaver, L.H.,Matthews, B.W.
      (1972) Biochem.Biophys.Res.Commun. 46: 1999
    • 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
    • Crystallographic Structural Analysis of Phosphoramidates as Inhibitors and Transition-State Analogs of Thermolysin
      Tronrud, D.E.,Monzingo, A.F.,Matthews, B.W.
      (1986) Eur.J.Biochem. 157: 261
    • 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
    • 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 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
    • 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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMOLYSIN
E
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
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
0ZN
Query on 0ZN

Download SDF File 
Download CCD File 
E
N-[(1R)-1-carboxy-3-phenylpropyl]-L-leucyl-L-tryptophan
C27 H33 N3 O5
PAPCSVADGJFRFM-HJOGWXRNSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000380 (0ZN)
Query on PRD_000380
EN-[(1S)-1-carboxy-3-phenylpropyl]-L-leucyl-L-tryptophanPeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0ZNKi: 50 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.171 
  • 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
OSCTSTdata reduction
EREFrefinement
AGROVATA/ROTAVATEdata scaling
RICHARDSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1989-01-09
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other