1TLP

CRYSTALLOGRAPHIC STRUCTURAL ANALYSIS OF PHOSPHORAMIDATES AS INHIBITORS AND TRANSITION-STATE ANALOGS OF THERMOLYSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 261-268

  • Primary Citation of Related Structures:  2TMN

  • PubMed Abstract: 
  • The mode of binding to thermolysin of the unsubstituted phosphoramidate inhibitor N-phosphoryl-L-leucinamide (P-Leu-NH2) has been determined crystallographically and refined at high resolution (R = 17.9% to 0.16-nm resolution). The mode of binding of ...

    The mode of binding to thermolysin of the unsubstituted phosphoramidate inhibitor N-phosphoryl-L-leucinamide (P-Leu-NH2) has been determined crystallographically and refined at high resolution (R = 17.9% to 0.16-nm resolution). The mode of binding of the naturally occurring thermolysin inhibitor phosphoramidon reported previously [Weaver, L. H., Kester, W. R. and Matthews, B. W. (1977) J. Mol. Biol. 114, 119-132] has also been confirmed by crystallographic refinement (R = 17.4% to 0.23-nm resolution). Phosphoramidon binds to the enzyme with a single oxygen of the phosphoramidate moiety as a zinc ligand. Together with three ligands to the metal from the protein the resultant complex has approximately tetrahedral geometry. However, in the case of P-Leu-NH2, two of the phosphoramidate oxygens interact with the zinc to form a complex that tends towards pentacoordinate. In this respect, P-Leu-NH2 appears to be a better transition-state analog than is phosphoramidon. In addition, the phosphorus-nitrogen bond length in P-Leu-NH2 is 0.18 nm, suggesting that the nitrogen is protonated whereas the same bond in phosphoramidon is much shorter (0.15 nm) suggesting that the nitrogen does not carry a charge. In phosphoramidon the distance from the phosphoramide nitrogen to Glu-143 is 0.39 nm whereas in P-Leu-NH2 this distance decreases to 0.34 nm. Taken together, these observations provide additional evidence in support of the participation of pentacoordinate intermediates in the mechanism of action of thermolysin [Holmes, M. A. and Matthews, B. W. (1981) Biochemistry 20, 6912-6920] and the role of Glu-143 in first promoting the attack of a water molecule on the carbonyl carbon of the scissile bond and subsequently acting as a 'proton shuttle' to transfer the proton to the leaving nitrogen [Monzingo, A. F. and Matthews, B. W. (1984) Biochemistry 23, 5724-5729; Hangauer, D. G., Monzingo, A. F. and Matthews, B. W. (1984) Biochemistry 23, 5730-5741].


    Related Citations: 
    • 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
    • Binding of Lanthanide Ions to Thermolysin
      Matthews, B.W.,Weaver, L.H.
      (1974) Biochemistry 13: 1719
    • Role of Calcium in the Thermal Stability of Thermolysin
      Dahlquist, F.W.,Long, J.W.,Bigbee, W.L.
      (1976) Biochemistry 15: 1103
    • The Gamma Turn. Evidence for a New Folded Conformation in Proteins
      Matthews, B.W.
      (1972) Macromolecules 5: 818
    • The Structure and Stability of Thermolysin
      Weaver, L.H.,Kester, W.R.,Teneyck, L.F.,Matthews, B.W.
      (1976) Experientia,Suppl. 26: 31
    • Comparison of the Structures of Carboxypeptidase a and Thermolysin
      Kester, W.R.,Matthews, B.W.
      (1977) J.Biol.Chem. 252: 7704
    • 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
      Matthews, B.W.,Colman, P.M.,Jansonius, J.N.,Titani, K.,Walsh, K.A.,Neurath, H.
      (1972) Nature New Biol. 238: 41
    • 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
    • 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 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
    • 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 Refined at 1.6 Angstroms Resolution
      Holmes, M.A.,Matthews, B.W.
      (1982) J.Mol.Biol. 160: 623
    • 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
    • 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
    • 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
    • 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
    • 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



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

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

Download SDF File 
Download CCD File 
E
N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
PHOSPHORAMIDON
C23 H34 N3 O10 P
ZPHBZEQOLSRPAK-XLCYBJAPSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000638 (RDF)
Query on PRD_000638
EPHOSPHORAMIDONGlycopeptide / Enzyme inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RDFKi: 28 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 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: 2008-05-22
    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