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Example of metalloproteases: thermolysin complex with DMS, acetate, Zn+2 and Ca+2, 2a7g

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Metalloproteases are proteases where the water molecule that is used for hydrolysis is complexed to a metal ion in the catalytic center of the enzyme. The metal ion is itself hold in position by several amino acid residues. The metalloproteases are one of seven superclans of the proteases in the UniProt/MEROPS classification.


A first raw classification is that into exo- and endopeptidases, according to whether the protein is cleaved at the end or not. The most advanced classification is that edited by UniProt and available at the MEROPS database (see link below). It lists 54 families of closely related metalloproteases that are grouped into 15 clans. We have chosen six examples from different clans that can be viewed by clicking on the green links, each with an additional center scene:

  • neutral zinc metallopeptidases, from Bac. stearothermophilus (2a7g, ). Matrix metalloproteinases and a lot of well-known other proteases belong to this big clan.
  • carboxypeptidases, (Bos taurus, 5cpa, )
  • insulinases, (E. coli, 1q2l, )
  • cytosol-aminopeptidases, (Bos taurus, 1lam, )
  • methionine-aminopeptidases, (2b3k, )
  • renal dipeptidases, (1itq, )

3D structures of metalloprotease


Matrix metalloproteinase


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Ralf Stephan, Michal Harel, David Canner

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