The Enzymes

thermophilus MnSOD, and the data showed that there were three phases to this reaction a fast burst phase of quick HO2 dismutation, a slower second phase, and a final fast phase (78). A dead-end form of the enzyme was implicated to account for the slow phase (78). This has been formulated as a side-on-bound Mn -peroxo species based on spectroscopic similarities to manganese model complexes with side-on-bound peroxy groups (83). Such phases are not observed for FeSOD (84). 

Most of the known dioxygenases contain iron, and these enzymes tend to be very specific in their function (87, 89). For example, the 

Manganese peroxidase (MnP) is an unique enzyme in many respects. It is an extracellular enzyme that involves a heme protoporphyrin IX for the oxidation of Mn to Mn 94, 95). A crystal structure at 2.06-A resolution of the manganese peroxidase from the white rot basidiomycete Phanerocaete chrysosporium, which utilizes this enzyme to degrade lignin, appeared in 1994 96). The active site (Fig. 5) and the overall structure are quite similar to lignin peroxidase (LiP), 

Oxalate and similar small molecule chelators play a key role in the 

Finally, there is a functional similarity between the MnP and LiP enzymes (110). LiP has been shown to be able to oxidize Mn (107). Further, it has been shown that a veratryl alcohol is produced in conjunction with LiP, and it has been suggested that this compound may serve LiP in a capacity similar to that served by Mn in MnP (109). 

Reaction 3.1, the key reaction of propionic acid fermentation, is catalyzed by pyruvate carboxytransphosphorylase, a unique biotin-dependent transcarboxylase (see below). There are other reactions of carboxyl group transfer catalyzed by phosphoenolpyruvate (PEP) carboxytransphosphorylase and phosphoenolpyruvate carboxykinase, but these (i) do not require biotin and (ii) use CO2 as the source of carboxyl groups. The actual species involved may be HCO3 (or H2CO3) rather than free CO2 (Cooper et al., 1968), since free CO2 is not evolved in the PEP carboxytransphosphorylase reaction (Swick and Wood, 1960). Propionic acid bacteria are able to decarboxylate succinate, producing CO2 in a biotin-dependent reaction (Delwiche,1948 Lichstein, 1958). If succinate is accumulated as the end product, then the cycle (see Fig. 3.1) is broken, and oxaloacetic acid is not supplied by reaction 3.1, but is formed primarily by CO2 fixation onto PEP catalyzed by PEP carboxytransphosphorylase (PEP-CTP). 

PEP carboxytransphosphorylase. The enzyme catalyzes the first reaction in the C02-fixation sequence, the major C02-fixing mechanism in propionibacteria  

It can be seen that the reaction requires an energy-rich compound, phosphoenolpyruvate, and inorganic orthophosphate (Pi), tiiat it is reversible and stimulated when pyrophosphatase is added (Siu and Wood, 1962). The rate of the forward reaction is seven times higher than the reverse reaction. In the absence of CO2 the enzyme catalyzes an irreversible conversion of PEP and inorganic phosphate to pyruvate and PPi (Lochmiiller et al., 1966)  

It is assumed that both the reactions are catalyzed by the complex of PEP-Pi-enzyme. CO2 competes for the complex, driving the reaction towards oxaloacetate and thus decreasing the rate of pyruvate production. Reaction 3.11 is irreversible under experimental conditions, but reaction 3.10 is reversible and interesting in that PPi can be used to form PEP from pyruvate (Davis and Wood, 1966). Therefore, the PPi derived from ATP can be reutilized, thus acting as a control mechanism for PEP preservation. And since PPi strongly inhibits the PEP carboxytransphosphorylase reaction, PEP can be diverted to the Krebs cycle (Frings and Schlegel, 1970). 

Under conditions unfavorable for transcarboxylation, CO2 fixation onto PEP becomes vitally important for bacteria, but the availability of PEP can limit the production of C4-compounds. Nevertheless, for this situation Nature supplied propionibacteria with the enzyme pyruvate-phosphate dikinase (Evans and Wood, 1968). The enzyme is induced by growth on lactate, it generates pyrophosphate and catalyzes the conversion of pyruvate to phosphoenolpyruvate in vivo. 

Functional mimic systems for the MnP enzyme will be discussed in Section V, Reactivity. An example of monomeric complexes prepared with a-hydroxy acids as functional mimics is presented in Section III.A.3 on monomeric structures. 

The FeRR system has been extensively studied (112, 114). For this type of ribonucleotide reductase, the enzyme is comprised of two subunits, known as R1 and R2 (or occasionally B1 and B2). The R1 and 

---

It now appears that many hormones (e.g. glucagon and adrenaline) in both animals and plants exert their effects by, as a first step, decreasing or increasing cyclic AMP within the cell. This may possibly occur by modification of the activity of the enzyme AMP cyclase which generates cyclic AMP from ATP. 

Enzymes often need for their activity the presence of a non-protein portion, which may be closely combined with the protein, in which case it is called a prosthetic group, or more loosely associated, in which case it is a coenzyme. Certain metals may be combined with the enzyme such as copper in ascorbic oxidase and selenium in glutathione peroxidase. Often the presence of other metals in solution, such as magnesium, are necessary for the action of particular enzymes. 

Enzymes are classified in terms of the reactions which they catalyse and were formerly named by adding the suffix ase to the substrate or to the process of the reaction. In order to clarify the confusing nomenclature a system has been developed by the International Union of Biochemistry and the International Union of Pure and Applied Chemistry (see Enzyme Nomenclature , Elsevier, 1973). The enzymes are classified into divisions based on the type of reaction catalysed and the particular substrate. The suffix ase is retained and recommended trivial names and systematic names for classification are usually given when quoting a particular enzyme. Any one particular enzyme has a specific code number based upon the new classification. 

Michaelis constant An experimentally determined parameter inversely indicative of the affinity of an enzyme for its substrate. For a constant enzyme concentration, the Michaelis constant is that substrate concentration at which the rate of reaction is half its maximum rate. In general, the Michaelis constant is equivalent to the dissociation constant of the enzyme-substrate complex. 

The enzymes may be classified under some of the above headings. 

Figure C1.5.17.(A) Enzymatic cycle of cholesterol oxidase, which catalyses tire oxidation of cholesterol by molecular oxygen. The enzyme s naturally fluorescent FAD active site is first reduced by a cholesterol substrate,...

All organisms seem to have an absolute need for magnesium. In plants, the magnesium complex chlorophyll is the prime agent in photosynthesis. In animals, magnesium functions as an enzyme activator the enzyme which catalyses the ATP hydrolysis mentioned above is an important example. 

Table 2 shows the results of our preliminary calculations of the pKa of the Cys403 residue, for several different models of the enzyme, based on two structures available from the PDB. In the case of the YPT structure, a crystal water molecule is close to Cys403 and was included in some of the calculations as part of the protein (i.e. it was treated with the same internal dielectric as that of the protein). Simulations denoted as -I-H2O in Table 2, include a crystallographically resolved, buried water molecule, situated 3.2lA from... 

R. C. Wade, M. E. Davis, B. A. Luty, J. D. Madura, and J. A. McCammon. Gating of the active site of triose phosphate isomerase Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys. J., 64 9-15, 1993. 

P. Derreumaux and T. Schlick. The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys. J., 74 72-81, 1998. 

Application of the CCM to small sets (n < 6) of enzyme inhibitors revealed correlations between the inhibitory activity and the chirality measure of the inhibitors, calculated by Eq. (26) for the entire structure or for the substructure that interacts with the enzyme (pharmacophore) [41], This was done for arylammonium inhibitors of trypsin, Di-dopamine receptor inhibitors, and organophosphate inhibitors of trypsin, acetylcholine esterase, and butyrylcholine esterase. Because the CCM values are equal for opposite enantiomers, the method had to be applied separately to the two families of enantiomers (R- and S-enantiomers). 

This poster indicates the structures of the compounds involved in a reaction, the enzymes catalyzing a reaction, the coenzymes and regulators involved, and whether such a reaction is a general pathway occurring in all species, or a pathway specific to higher plants, animals, or unicellular organisms. 

This is exactly what we have done [21], For each reaction the constitution and stereochemistry of the reaction partners, the coenzymes, and regulators were stored as connection tables (as far as they were known), and the enzymes by name and EC number. 

This means that the methods developed for the calculation of physicochemical effects can also be used to deepen our understanding of biochemical rcaaions. Clearly, electronic effects within the substrate molecule arc not the only ones determining its reactivity, The binding of the substrate to the enzyme is also influenced... 

---