Experimental Data Snapshot

  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history


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:  

  • 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 ...

    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: 
    • 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
    • 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
    • The Conformation of Thermolysin
      Matthews, B.W.,Weaver, L.H.,Kester, W.R.
      (1974) J.Biol.Chem. 249: 8030
    • 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
    • Structure of Thermolysin Refined at 1.6 Angstroms Resolution
      Holmes, M.A.,Matthews, B.W.
      (1982) J.Mol.Biol. 160: 623
    • 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 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 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
    • Role of Calcium in the Thermal Stability of Thermolysin
      Dahlquist, F.W.,Long, J.W.,Bigbee, W.L.
      (1976) Biochemistry 15: 1103
    • Binding of Lanthanide Ions to Thermolysin
      Matthews, B.W.,Weaver, L.H.
      (1974) Biochemistry 13: 1719
    • 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 Hydroxamic Acid Inhibitors to Crystalline Thermolysin Suggests a Pentacoordinate Zinc Intermediate in Catalysis
      Holmes, M.A.,Matthews, B.W.
      (1981) Biochemistry 20: 6912
    • 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
    • Amino-Acid Sequence of Thermolysin
      Titani, K.,Hermodson, M.A.,Ericsson, L.H.,Walsh, K.A.,Neurath, H.
      (1972) Nature New Biol. 238: 35

    Organizational Affiliation

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


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on CA

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 Ligand Interaction
Query on LYS

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C6 H15 N2 O2
 Ligand Interaction
Query on VAL

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C5 H11 N O2
 Ligand Interaction
Query on FE

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 Ligand Interaction
Query on DMS

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C2 H6 O S
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 1.8 Å
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.600α = 90.00
b = 93.600β = 90.00
c = 131.600γ = 120.00
Software Package:
Software NamePurpose
NIELSENdata reduction
XUONG)data scaling
NIELSENdata scaling
XENGENdata scaling
XUONG)data reduction
XENGENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

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