Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Observed: 0.170 

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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

  • DOI: 10.1021/bi00400a008
  • Primary Citation of Related Structures:  
    4TMN, 5TMN

  • 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: 
    • 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
    • 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 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
    • 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
    • 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
    • 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
    • Structure of Thermolysin Refined at 1.6 Angstroms Resolution
      Holmes, M.A., Matthews, B.W.
      (1982) J Mol Biol 160: 623
    • 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 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
    • 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
    • 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
    • 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 U S A 72: 4341
    • The Structure and Stability of Thermolysin
      Weaver, L.H., Kester, W.R., Teneyck, L.F., Matthews, B.W.
      (1976) Experientia Suppl 26: 31
    • 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
    • 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
    • Amino-Acid Sequence of Thermolysin
      Titani, K., Hermodson, M.A., Ericsson, L.H., Walsh, K.A., Neurath, H.
      (1972) Nature New Biol 238: 35
    • 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
    • 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
    • The Gamma Turn. Evidence for a New Folded Conformation in Proteins
      Matthews, B.W.
      (1972) Macromolecules 5: 818
    • 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

    Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THERMOLYSINE316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on 0PK

Download CCD File 
C25 H34 N3 O7 P
 Ligand Interaction
Query on ZN

Download CCD File 
 Ligand Interaction
Query on CA

Download CCD File 
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0PKKi:  0.06800000369548798   nM  Binding MOAD
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000656 (0PK)
Query on PRD_000656
ECBZ-PHE-P-LEU-ALA (ZFPLA)Peptide-like /  Enzyme inhibitor


Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Observed: 0.170 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.1α = 90
b = 94.1β = 90
c = 131.4γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1989-01-09
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-06-13
    Changes: Derived calculations
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2017-11-29
    Changes: Derived calculations, Other