4TMN

SLOW-AND FAST-BINDING INHIBITORS OF THERMOLYSIN DISPLAY DIFFERENT MODES OF BINDING. CRYSTALLOGRAPHIC ANALYSIS OF EXTENDED PHOSPHONAMIDATE TRANSITION-STATE ANALOGUES


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Slow- and fast-binding inhibitors of thermolysin display different modes of binding: crystallographic analysis of extended phosphonamidate transition-state analogues.

Holden, H.M.Tronrud, D.E.Monzingo, A.F.Weaver, L.H.Matthews, B.W.

(1987) Biochemistry 26: 8542-8553

  • Primary Citation of Related Structures:  5TMN, 7TMN

  • PubMed Abstract: 
  • The modes of binding to thermolysin of two phosphonamidate peptide inhibitors, carbobenzoxy-GlyP-L-Leu-L-Leu (ZGPLL) and carbobenzoxy-L-PheP-L-Leu-L-Ala (ZFPLA), have been determined by X-ray crystallography and refined at high resolution to crystall ...

    The modes of binding to thermolysin of two phosphonamidate peptide inhibitors, carbobenzoxy-GlyP-L-Leu-L-Leu (ZGPLL) and carbobenzoxy-L-PheP-L-Leu-L-Ala (ZFPLA), have been determined by X-ray crystallography and refined at high resolution to crystallographic R-values of 17.7% and 17.0%, respectively. (GlyP is used to indicate that the trigonal carbon of the peptide linkage is replaced by the tetrahedral phosphorus of a phosphonamidate group.). These inhibitors were designed to be structural analogues of the presumed catalytic transition state and are potent inhibitors of thermolysin (ZGPLL, Ki = 9.1 nM; ZFPLA, Ki = 0.068 nM) [Bartlett, P. A., & Marlowe, C. K. (1987) Biochemistry (following paper in this issue)]. ZFPLA binds to thermolysin in the manner expected for the transition state and, for the first time, provides direct support for the presumed mode of binding of extended substrates in the S2 subsite. The mode of binding of ZFPLA displays all the interactions that are presumed to stabilize the transition state and supports the postulated mechanism of catalysis [Hangauer, D. G., Monzingo, A. F., & Matthews, B. W. (1984) Biochemistry 23, 5730-5741]. The two oxygens of the phosphonamidate moiety are liganded to the zinc to give overall pentacoordination of the metal. For the second inhibitor the situation is different. Although both ZFPLA and ZGPLL have similar modes of binding in the S1' and S2' subsites, the configurations of the carbobenzoxy-Phe and carbobenzoxy-Gly moieties are different. For ZFPLA the carbonyl group of the carbobenzoxy group is hydrogen bonded directly to the enzyme, whereas in ZGPLL the carbonyl group is rotated 117 degrees, and there is a water molecule interposed between the inhibitor and the enzyme. For ZGPLL only one of the phosphonamidate oxygens is liganded to the zinc. Correlated with the change in inhibitor-zinc ligation from monodentate in ZGPLL to bidentate in ZFPLA there is an increase in the phosphorus-nitrogen bond length of about 0.25 A, strongly suggesting that the phosphonamide nitrogen in ZFPLA is cationic, analogous to the doubly protonated nitrogen of the transition state. The observation that the nitrogen of ZFPLA appears to donate two hydrogen bonds to the protein also indicates that it is cationic. The different configurations adopted by the respective inhibitors are correlated with large differences in their kinetics of binding [Bartlett, P. A., & Marlowe, C. K. (1987) Biochemistry (following paper in this issue)]. These differences in kinetics are not associated with any significant conformational change on the part of the enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • 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
    • 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
    • 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
    • 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
    • Binding of N-Carboxymethyl Dipepetide 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
    • 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
    • Binding of Lanthanide Ions to Thermolysin
      Matthews, B.W.,Weaver, L.H.
      (1974) Biochemistry 13: 1719
    • 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
    • Role of Calcium in the Thermal Stability of Thermolysin
      Dahlquist, F.W.,Long, J.W.,Bigbee, W.L.
      (1976) Biochemistry 15: 1103
    • 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
    • Comparison of the Structures of Carboxypeptidase a and Thermolysin
      Kester, W.R.,Matthews, B.W.
      (1977) J.Biol.Chem. 252: 7704
    • 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
    • The Structure and Stability of Thermolysin
      Weaver, L.H.,Kester, W.R.,Teneyck, L.F.,Matthews, B.W.
      (1976) Experientia,Suppl. 26: 31
    • 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
    • The Conformation of Thermolysin
      Matthews, B.W.,Weaver, L.H.,Kester, W.R.
      (1974) J.Biol.Chem. 249: 8030
    • 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
    • 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
    • The Gamma Turn. Evidence for a New Folded Conformation in Proteins
      Matthews, B.W.
      (1972) Macromolecules 5: 818
    • Amino-Acid Sequence of Thermolysin
      Titani, K.,Hermodson, M.A.,Ericsson, L.H.,Walsh, K.A.,Neurath, H.
      (1972) Nature New Biol. 238: 35
    • 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
    • Structure of Thermolysin Refined at 1.6 Angstroms Resolution
      Holmes, M.A.,Matthews, B.W.
      (1982) J.Mol.Biol. 160: 623
    • 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


    Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene 97403.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMOLYSIN
E
316Bacillus thermoproteolyticusGene 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

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

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Download CCD File 
E
N-[(S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}-2-phenylethyl](hydroxy)phosphoryl]-L-leucyl-L-alanine
ZFPLA
C25 H34 N3 O7 P
PREBTZMCCRSQJI-YUXAGFNASA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000656 (0PK)
Query on PRD_000656
ECBZ-PHE-P-LEU-ALA (ZFPLA)Peptide-like / Enzyme inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0PKKi: 0.068 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.100α = 90.00
b = 94.100β = 90.00
c = 131.400γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement

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: 2012-06-13
    Type: Derived calculations
  • Version 1.4: 2012-12-12
    Type: Other
  • Version 1.5: 2017-11-29
    Type: Derived calculations, Other