Enzyme Mechanism - Examples
Part III. Metal Ion Assisted Catalysis
Many enzymes are assisted by metal ions
Fe2+ /Fe3+ Cu2+ Zn2+ Mn2+ Co2+
Other enzymes are 'activated' by metal ions
Na+ K+ Mg2+ Ca2+
Activation changes enzyme shape without the metal ion being involved in catalysis.
Endoproteases (ones that cut in the middle of a peptide chain) like thermolysin use Zn2+. So do exoproteases (ones that chew in from the carboxy-terminal end) like carboxypeptidase. How do Zn-proteases catalyze peptide bond hydrolysis?
Thermolysin's Zn2+ coordinates the substrate's carbonyl while Glu-143 activates water, which attacks the substrate.
Figure 8. Model catalytic mechanism for peptide bond hydrolysis as catalyzed by the endoprotease thermolysin, which is an enzyme found in some laundry detergents where it is used to help remove protein stains from your clothes.
Carboxypeptidase works in a similar way.
Figure 9. Model of the active site of the exoprotease carboxypeptidase showing the role of Zn2+ in activating the substrate molecule by binding the carbonyl oxygen, which would make the peptide bond more easily hydrolyzed.
So these proteases depend more on activation of the substrate in a way more like the H+ catalysis of ester hydrolysis, rather than generating a very strong nucleophile (i.e. Ser-194) like in the serine proteases.
Another example of metal ion assisted enzyme catalysis is carbonic anhydrase, which catalyzes the hydration of carbon dioxide leading to the formation of bicarbonate. Carbonic anhydrase is an enzyme with a very high catalytic rate, one of the highest known. Carbonic anhydrase is used to balance the pH in the kidney during filtration of urine from the serum. In this case, a Zn2+ is bound by 3 His side chains of the enzyme and a water molecule is also bound to the metal ion, as shown below:
Figure 10. The active site of carbonic anhydrase.
Figure from Voet's Biochemistry, copyright ©1990, John Wiley & Sons, Inc.
The role of Zn2+ in the carbonic anhydrase active site has been suggested to help activate the bound water molecule to generate a hydroxide ion which can attack carbon dioxide to directly make bicarbonate. The Zn2+ is assisted in removing a proton from water by nearby acidic side chains (Glu-106 or Glu-117 as shown above in the model of carbonic anhydrase's active site - see Fig. 10). The proposed catalytic mechanism of carbonic anhydrase is shown below:
Figure 11. The catalytic mechanism of carbonic anhydrase emphasizing the role of Zn2+. After the gaseous carbon dioxide is attacked by the hydroxide ion bound to Zn2+ and the intermediate forms, a water molecule displaces the bicarbonate and replaces the hydroxide ion bound to Zn2+. In this process, a proton is generated which can be used to balance the pH during the function of the kidney.
Figure from Voet's Biochemistry, copyright ©1990, John Wiley & Sons, Inc.
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©Wilbur H. Campbell, 1995; wcampbel@mtu.edu