4 Examples of enzymes
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1 Catalysis 1
2 4 Examples of enzymes Adding water to a substrate: Serine proteases. Carbonic anhydrase. Restrictions Endonuclease. Transfer of a Phosphoryl group from ATP to a nucleotide. Nucleoside monophosphate (NMP) kinase. 2
3 4 different challenges Serine proteases - chymotrypsin: promoting a reaction that is immeasurably slow at neutral ph. Carbonic anhydrase: Making a fast reaction even faster. Restrictions Endonucleases - EcoRV: attaining a high level of specificity. NMP kinase: Transfer of a Phosphoryl group from ATP to a nucleotide and not to water. 3
4 4 strategies for catalysis 1. Covalent catalysis. 2. General acid-base catalysis. 3. Metal ion catalysis. 4. Catalysis by approximation. They are not mutually exclusive! 4
5 1. Covalent catalysis The active site usually contains a powerful nucleophile. The nucleophile is temporarily covalently bound to the substrate. Chymotrypsin is a good example. 5
6 2. General acid-base catalysis An acid or a base plays the role of a proton donor or acceptor. Not water. Again chymotrypsin s active site is a good example 6
7 3. Metal ion catalysis Metals are good electrophilic catalysts stabilizing negative charges. They can also generate a nucleophile by increasing the acidity of an adjacent molecule (e.g. Carbonic anhydrase). The metal may bind the substrate to increase the binding energy (e.g. NMP kinase). 7
8 4. Catalysis by approximation Bringing two substrates close together. NMP kinase brings two nucleotides close together so that the transfer of the Phosphoryl group is from one to the other. 8
9 1. Proteases Proteases Proteins must have a certain turnover rate. Many regulatory steps are achieved by the concerted breakdown of proteins (e.g. cell cycle). Unfolded proteins are also degraded, so as not to cause any problems. In the gut proteins are broken down to their amino acid components. 9
10 1. Proteases The proteolytic reaction Addition of water to the peptide bond. R O C N H R' O + H 2 O + R C O R' NH 3 + The reaction is thermodynamically favored. In the absence of a catalysis at neutral ph however, t 1/2 may be as long as hundreds of years. 10
11 1. Proteases Chymotrypsin Chymotrypsin cleaves peptide bonds on the C- terminal side of large hydrophobics. It is a good example of covalent modification as a catalytic strategy. 11
12 1. Proteases What is the nucleophile? Reactions with organofluorophosphates (e.g. DIPF) selectively labels Ser
13 1. Proteases Monitoring kinetics 13
14 1. Proteases Kinetic analysis 14
15 1. Proteases A reaction in two stages A. Acyl enzyme intermediate formation releasing the amine. B. Hydrolysis of the acyl enzyme releasing the COO -. 15
16 1. Proteases 16
17 1. Proteases 17
18 1. Proteases The catalytic triad Asp 102 increases the catalytic power of H57. His 57 serves as a general base catalyst. Thus an alkoxide is formed which is a much stronger nucleophile than a hydroxyl. 18
19 1. Proteases The reaction as a whole 19
20 1. Proteases Step 1 Substrate binds. Nucleophilic attack of the alkoxide on the peptide carbonyl carbon. 20
21 1. Proteases Step 2 A change in the geometry of the peptide bond from trigonal planer to tetrahedral. 21
22 1. Proteases Step 2 cont. The formal negative charge on the carbonyl oxygen is stabilized by the oxyanion hole. 22
23 1. Proteases Step 3 Collapse to an acyl enzyme intermediate. 23
24 1. Proteases Step 4 The amine group leaves the enzyme. Thus half of the substrate remains bound to the enzyme. 24
25 1. Proteases Step 5 A water molecules replaces the amine. His 57 acts as a general base catalyst again activating the water molecule. It now undertakes a nucleophilic attack on the acyl carbon. 25
26 1. Proteases Step 6 Formation of an unstable tetrahedral intermediate. 26
27 1. Proteases Step 7 The tetrahedral intermediate breaks down. 27
28 1. Proteases Step 8 Release of the carboxylic acid. The cycle is now complete. 28
29 1. Proteases Specificity cause A hydrophobic pocket selectively binds large hydrophobic amino acids. Trypsin and elastase contain other pockets defining their specificity. 29
30 1. Proteases 30
31 1. Proteases 31
32 1. Proteases Different serine proteases: 1. Subtilisin 32
33 1. Proteases Different serine proteases: 2. Carboxypeptidase II Thus, the catalytic triad has appeared at least 3 times during the course of evolution! 33
34 2. Carbonic anhydrase Carbonic anhydrase (CA) CA catalyses the hydration and dehydration of CO 2. 34
35 2. Carbonic anhydrase CA s importance The natural rate of the reactions is fast: k 1 = 0.15 s -1, however it is not fast enough. In the presence of the enzyme k cat = 10 6 s -1. The need for the enzyme arises from the fact that at times we need CO 2 (e.g. in the lungs) and at time bicarbonate. 35
36 2. Carbonic anhydrase CA and Zinc CA was the first enzyme known to contain Zinc. Now as much as 1/3 of all enzymes are known to contain bound metal ions. Zinc is found in biology only as Zn 2+. It is normally coordinated by four ligands. Remember that coordination is when one of the partners in the bond donates the pair of electrons entirely. 36
37 2. Carbonic anhydrase Due to the coordination the net charge due to the Zn 2+ is
38 2. Carbonic anhydrase Catalysis and ph The midpoint in the transition is around ph 7. Thus a group with a pk A of 7 is critical to the enzyme s activity. It is not a Histidine but rather a water molecule k cat (10 6 s -1 ) 38
39 2. Carbonic anhydrase Thus the binding of water to Zn 2+ lowers the water s pk A from 15.4 to 7. 39
40 2. Carbonic anhydrase The mechanism 40
41 2. Carbonic anhydrase Step 1 Zn 2+ facilitates the release of a H + from the bound water molecule. 41
42 2. Carbonic anhydrase Step 2 The CO 2 binds in the enzyme s active site. It is positioned accordingly for the attack. 42
43 2. Carbonic anhydrase Step 3 Nucleophilic attack by the hydroxide ion. The CO 2 is converted to bicarbonate ion. 43
44 2. Carbonic anhydrase Step 4 Regeneration of the catalytic site though the exchange of water and the release of bicarbonate. 44
45 2. Carbonic anhydrase The proton paradox One of the steps in the reaction involves the deprotonation of the water to form a hydroxide ion. When the enzyme is working in the opposite direction (dehydration of bicarbonate) the hydroxide ion protonates to form water. 45
46 2. Carbonic anhydrase The proton paradox cont. Proton diffusion in water is very rapid, with second order rate constants of M -1 s -1. Thus k -1 must be lower than M -1 s -1. The equilibrium constant for H + release, K = k 1 /k -1 =10-7 M. Thus k 1 must be equal to 10 4 s -1. In other words, the rate of H + diffusion limits the rate of H + release to less than 10 4 s -1 for a group with a pka= 7. 46
47 2. Carbonic anhydrase The proton paradox cont. However if CO 2 is hydrated at a rate constant of 10 6 s -1 then every step in the reaction must proceed at least as fast. How can this be if the rate of proton release is only 10 4 s -1? How can this apparent paradox be resolved? 47
48 2. Carbonic anhydrase The proton shuffle The resolution of the paradox was possible upon noticing that maximal acceleration of the hydration reaction was only possible in the presence of buffer. The reason is that the [H + ] is only 10-7 M, but the concentration of the buffer can be much higher. 48
49 2. Carbonic anhydrase The proton shuffle cont. If the buffer (BH + ) has a pk A of 7 (similar to the water molecule bound to the Zn 2+ ) then the following equilibrium constant is obtained: 49
50 2. Carbonic anhydrase The proton shuffle cont. Now the rate of deprotonation k 1 (or the rate of H + abstraction by the buffer) will be equal to: k 1 [B]. The second order rate constants k 1 and k -1 will be limited by buffer diffusion to values less than 10 9 M -1 s -1. Thus, [B] higher than 10-3 M will be able to support rate constant for hydration of CO 2 of 10 6 s -1. This is because: k 1 [B] = (10 9 M -1 s -1 ) (10-3 M) = 10 6 s
51 2. Carbonic anhydrase The proton shuffle cont. Experimental date supports this prediction. 51
52 2. Carbonic anhydrase So what is the buffer? Most buffers are too big to reach the active site of the enzyme. For this reason the enzyme has positioned a His residue to act as the buffer in close proximity: a built-in H + shuffle. 52
53 2. Carbonic anhydrase A built-in proton shuffle So the enzyme has evolved a mechanism to control H + release and uptake to dramatically accelerate the rate of the reaction. This is seen in many other instances in which enzymes use acid-base catalysis. It also explains the prominence of such catalytic mechanisms. 53
54 2. Carbonic anhydrase Evolution of Zn 2+ active sites The enzymes referred to so far are called α- carbonic anhydrases (α-cas). Bacteria and pants contain β-cas that are distinct from α-cas, although they contain Zn 2+ in their active site. The ligands for Zn 2+ are 1 His and 2 Cys residues, as opposed to 3 His in α-cas. 54
55 4. NMP kinases Nucleotide monophosphate kinases Nucleotide monophosphate (NMP) kinases catalyze the reversible transfer of a Phosphoryl from an NTP to an NMP. They can also be used to generate some NTP from two NDPs when NTP concentrations is being exhausted. Remember that: [ATP] > [ADP] > [AMP] 55
56 4. NMP kinases 56
57 4. NMP kinases Adenylate kinase We will concentrate on adenylate kinase. Its biggest challenge is to transfer the Phosphoryl group to an AMP and avoid the competing reaction - hydrolysis. It provides an example for: Induced fit. Metal ion catalysis which is different than the one used by the other enzymes previously discussed. 57
58 4. NMP kinases NMP kinases form a family 58
59 4. NMP kinases A core domain of an NMP kinase 59
60 4. NMP kinases The P-loop: G-XXXX-G-K 60
61 4. NMP kinases What is the real substrate? The affinity of NTPs for Mg 2+ (or Mn 2+ ) is 10-4 M. Since [Mg 2+ ]~10-3 in the cell all NTPs are found as: NTP-Mg 2+ 61
62 4. NMP kinases How does it affect catalysis? Mg 2+ neutralizes the charge on the NTP to minimize non-specific interactions. The interactions between the Mg 2+ and the NTP hold it in a stable conformation ready for catalysis. It provides for additional possibilities for interaction with the enzyme thereby increasing the binding energy. 62
63 4. NMP kinases In some enzymes the Mg 2+ is bound directly to the side chains (often E or D). In other there are bridging water molecules. 63
64 4. NMP kinases Binding induces a big conformational change The binding of ATP causes a large conformational change in the protein. The P-loop closes down on the ATP interacting with the β- phosphate. The movement of the P-loop enables the top domain of the protein to move closing down on the substrate further. 64
65 4. NMP kinases Catalysis Once the ATP is bound its γ-phosphate ions are positioned exactly near the AMP ready for catalysis. Binding of the AMP causes additional conformational change in the protein. Without the binding of both substrates the reaction will not take place. This is how hydrolysis is prevented. 65
66 4. NMP kinases P-loop conservation 66
67 4. NMP kinases P-loop conservation cont. 67
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