1LNE

A STRUCTURAL ANALYSIS OF METAL SUBSTITUTIONS IN THERMOLYSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structural analysis of zinc substitutions in the active site of thermolysin.

Holland, D.R.Hausrath, A.C.Juers, D.Matthews, B.W.

(1995) Protein Sci 4: 1955-1965

  • DOI: 10.1002/pro.5560041001
  • Primary Citation of Related Structures:  
    1LNF, 1LNE, 1LND, 1LNC, 1LNB, 1LNA

  • PubMed Abstract: 
  • Native thermolysin binds a single catalytically essential zinc ion that is tetrahedrally coordinated by three protein ligands and a water molecule. During catalysis the zinc ligation is thought to change from fourfold to fivefold. Substitution of the active-site zinc with Cd2+, Mn2+, Fe2+, and Co2+ alters the catalytic activity (Holmquist B, Vallee BL, 1974, J Biol Chem 249:4601-4607) ...

    Native thermolysin binds a single catalytically essential zinc ion that is tetrahedrally coordinated by three protein ligands and a water molecule. During catalysis the zinc ligation is thought to change from fourfold to fivefold. Substitution of the active-site zinc with Cd2+, Mn2+, Fe2+, and Co2+ alters the catalytic activity (Holmquist B, Vallee BL, 1974, J Biol Chem 249:4601-4607). Excess zinc inhibits the enzyme. To investigate the structural basis of these changes in activity, we have determined the structures of a series of metal-substituted thermolysins at 1.7-1.9 A resolution. The structure of the Co(2+)-substituted enzyme is shown to be very similar to that of wild type except that two solvent molecules are liganded to the metal at positions that are thought to be occupied by the two oxygens of the hydrated scissile peptide in the transition state. Thus, the enhanced activity toward some substrates of the cobalt-relative to the zinc-substituted enzyme may be due to enhanced stabilization of the transition state. The ability of Zn2+ and Co2+ to accept tetrahedral coordination in the Michaelis complex, as well as fivefold coordination in the transition state, may also contribute to their effectiveness in catalysis. The Cd(2+)- and Mn(2+)-substituted thermolysins display conformational changes that disrupt the active site to varying degrees and could explain the associated reduction of activity. The conformational changes involve not only the essential catalytic residue, Glu 143, but also concerted side-chain rotations in the adjacent residues Met 120 and Leu 144. Some of these side-chain movements are similar to adjustments that have been observed previously in association with the "hinge-bending" motion that is presumed to occur during catalysis by the zinc endoproteases. In the presence of excess zinc, a second zinc ion is observed to bind at His 231 within 3.2 A of the zinc bound to native thermolysin, explaining the inhibitory effect.


    Related Citations: 
    • Structural Comparison Suggests that Thermolysin and Related Neutral Proteases Undergo Hinge-Bending Motion During Catalysis
      Holland, D.R., Tronrud, D.E., Pley, H.W., Flaherty, K.M., Stark, W., Jansonius, J.N., Mckay, D.B., Matthews, B.W.
      (1992) Biochemistry 31: 11310
    • Structure of Thermolysin Refined at 1.6 Angstroms Resolution
      Holmes, M.A., Matthews, B.W.
      (1982) J Mol Biol 160: 623
    • 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
    • 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 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

    Organizational Affiliation

    Howard Hughes Medical Institute, University of Oregon, Eugene 97403, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THERMOLYSINA [auth E]316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.160 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.888α = 90
b = 93.888β = 90
c = 131.164γ = 120
Software Package:
Software NamePurpose
TNTrefinement
XENGENdata reduction
NIELSENdata reduction
XUONG)data reduction
XENGENdata scaling
NIELSENdata scaling
XUONG)data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-05-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-06-13
    Changes: Derived calculations
  • Version 1.4: 2012-07-18
    Changes: Non-polymer description
  • Version 1.5: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.6: 2018-04-04
    Changes: Data collection