Active sites coordination

Figure 12.8 Some other active-site coordination motifs in mononuclear zinc enzymes from left to right bacteriophage T7 lysozyme, 5-aminolaevulinate dehydratase, Ada DNA repair protein. (Reprinted with permission from Parkin, 2004. Copyright (2004) American Chemical Society.)...

FIGURE 13.23 Active site coordination geometry of plant LOXs. (Adopted from Andreou Feussner, 2009.)... 

The terminal step in methane generation by several methanogenic organisms, of which the best studied is the archaeon Methanobacterium thermoautotrophicum, is catalyzed by the enzyme S-methyl coenzyme M reductase (methylreductase, EC 1.8.-.-). This enzyme contains a macrocyclic tetrapyrrole-derived cofactor, F430, at the active site coordinating Ni(II) in the resting state. A Ni(I) state (Ni1F430) has been proposed as the active form of the cofactor. Extensive mechanistic and spectroscopic studies have been performed on the holoenzyme, isolated cofactor, and various synthetic model compounds. These studies are summarized in... 

Carbonic anhydrase (CA) is a zinc metalloenzyme involved in mammalian respiration, which catalyzes the hydration of carbon dioxide. Copper-complexed TPPC, competitively inhibits CA enzymatic activity as does copper-complexed TPPSj [32]. Experiments comparing the spectrophotometric characteristics of the two porphyrins in the presence of CA and apo-CA indicate that the zinc atoms in the active site of the enzyme are indeed involved in the interaction between the porphyrins and the enzyme. The metal-free porphyrins TPPSj and TPPC, do not inhibit the enzymatic activity of CA. Further, the spectrophotometric characteristics of these porphyrins in the presence of apo-CA were identical to those in the presence of wild-type CA, indicating the lack of involvement of the active site-coordinated zinc in the porphyrin-enzyme interaction for metal-free porphyrins. 

Figure 1.2 Top bond line drawings for the oxidized and reduced members of the three canonical pyranopterin Mo enzyme families (SO, DMSOR and XO). Bottom active site coordination geometries for SO, DMSOR, and XO as determined by X-ray crystallography.

Fraction of the active site coordinated with the monomer ... 

Fraction of active sites coordinated with components of metal Groups 1-111 ... 

The active site coordinates have to be supplied properly. In case of multi-domain proteins, extra caution needs to be exercised to define the active site. 

Molecular mechanics potential energy functions have been used to calculate binding constants, protein folding kinetics, protonation equilibria, active site coordinates, and to design binding sites [4,5]. 

Type n aldolases are found predominantly in bacteria and fungi, and are Zn " -dependent enzymes (Scheme 2.182) [1378]. Their mechanism of action was recently affirmed to proceed through a metal-enolate [1379] an essential Zn " atom in the active site (coordinated by three nitrogen atoms of histidine residues [1380]) binds the donor via the hydroxyl and carbonyl groups. This facilitates pro-(/ )-proton abstraction from the donor (presumably by a glutamic acid residue acting as base), rendering an enolate, which launches a nucleophilic attack onto the aldehydic acceptor. 

The amino acid His-350 is located in a position similar to the general acid/base aspartic acid of exosialidases (Fig. 3a Nani 291) and has been mutated to alanine for co-crystaUization with DP5 [106]. In comparison to wild type endoNF, the alanine residue red in Fig. 3a) H350A perfectly superposes with the Ca and C(5 atoms of the histidine residue. Thus, the backbone of the p-propeller is not affected by this mutation. In the H350A mutant, a trimeric sialic acid (DP3) is bound in the active site coordinated by a network of water molecules and polar contacts (Fig. 3c). The geometry of the active site constrains the otherwise helical polysialic acid into an extended conformation (see Sect. 8 for heUcal epitopes). 

Although Z.N. catalysts are very sensitive to polar substituents which tend to clock active sites, coordination polymerization by modified complexes is of course not limited to unsaturated hydrocarbons. A few examples are discussed hereafter which have put in evidence interesting new concepts. 

Fig. 8.1 Active-site coordination environments found in representative mononuclear zinc-containing enzymes. The pfQ value for peptide deformylase was measured using a Co(ll)-substituted mutant enzyme (E133A) [23].

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