Bacterially catalyzed

These processes are catalyzed by bacteria and probably involve both inorganic and organic iron and manganese species (22). They may also be strongly controlled by microbial competition between Fe(III) and sulfate-reducing bacteria (27). Associated with these reduction reactions is the reduction of residual sulfate (produced in the oxic zone by bacterially catalyzed reactions) similar to eq 7 (21). 

Sulfide-mineral oxidation by microbial populations has been postulated to proceed via direct or indirect mechanisms (Tributsch and Bennett, 1981a,b Boon and Heijnen, 2001 Fowler, 2001 Sand et al., 2001 Tributsch, 2001). In the direct mechanism, it is assumed that the action taken by the attached cell or bacterium on a metal sulfide will solubilize the mineral surface through direct enzymatic oxidation reactions. The sulfur moiety on the mineral surface is oxidized to sulfate without the production of any detectable intermediates. The indirect mechanism assumes that the cell or bacteria do not act directly on the sulfide-mineral surface, but catalyze reactions proximal to the mineral surface. The products of these bacterially catalyzed reactions act on the mineral surfaces to promote oxidation of the dissolved Fe(II) and S° that are generated via chemical oxidative processes. Ferrous iron and S°, present at the mineral surface, are biologically oxidized to Fe(III) and sulfate. Physical attachment is not required for the bacterial catalysis to occur. The resulting catalysis promotes chemical oxidation of the sulfide-mineral surface, perpetuating the sulfide oxidation process (Figure 1). 

Bacterial attack on the mineral may also enhance reaction with Fe(III) by exposing fresh surfaces. Such rate enhancement will also be achieved through the bacterially catalyzed oxidation and removal of the elemental sulfur produced in Eqs. (6)-(8). This reaction may be mediated by Fe(III) (25, 65). 

The second step is the reduction of nitrate to nitrogen gas. This reaction is also bacterially catalyzed, in this case by denitrifying bacteria, and requires a carbon source and a reducing agent such as methanol, CH3OH, or an organic carbon source, CH2O ... 

The bacterially-catalyzed oxidation of iron(II) to iron(III) by bacteria can result in... 

Iron Sulfur Compounds. Many molecular compounds (18—20) are known in which iron is tetrahedraHy coordinated by a combination of thiolate and sulfide donors. Of the 10 or more stmcturaHy characterized classes of Fe—S compounds, the four shown in Figure 1 are known to occur in proteins. The mononuclear iron site REPLACE occurs in the one-iron bacterial electron-transfer protein mbredoxin. The [2Fe—2S] (10) and [4Fe—4S] (12) cubane stmctures are found in the 2-, 4-, and 8-iron ferredoxins, which are also electron-transfer proteins. The [3Fe—4S] voided cubane stmcture (11) has been found in some ferredoxins and in the inactive form of aconitase, the enzyme which catalyzes the stereospecific hydration—rehydration of citrate to isocitrate in the Krebs cycle. In addition, enzymes are known that contain either other types of iron sulfur clusters or iron sulfur clusters that include other metals. Examples include nitrogenase, which reduces N2 to NH at a MoFe Sg homocitrate cluster carbon monoxide dehydrogenase, which assembles acetyl-coenzyme A (acetyl-CoA) at a FeNiS site and hydrogenases, which catalyze the reversible reduction of protons to hydrogen gas. 

Bacterial concentrations have also been determined by using the enzyme-catalyzed chemiluminescent reaction of reduced flavin mononucleotide (FMN) with oxygen and aldehydes. The detection limit was reported to be 10 ceUs of E. coli, which contains 7 x 10 g of FMN per ceU (303). 

Luminol chemiluminescence has also been recommended for measuring bacteria populations (304,305). The luminol—hydrogen peroxide reaction is catalyzed by the iron porphyrins contained in bacteria, and the light intensity is proportional to the bacterial concentration. The method is rapid, especially compared to the two-day period required by the microbiological plate-count method, and it correlates weU with the latter when used to determine bacteria... 

H-Dealkylation. This is commonly observed as a primary transformation of pesticides with A/-alkyl substituents, such as atrazine [1912-24-9] (3) (eq. 5), trifluraHn [1582-09-8] (4) (eq. 6) (16), and 3 -ethyl dipropylthiocarbamate [759-94-4] (EPTC) (5) (eq. 7) (18). These reactions are catalyzed by a variety of bacterial strains, including Noeardia, Pseudomonas, Phodococcus, and Streptomyces. 

Inhibitors as well as substrates bind in this crevice between the domains. From the numerous studies of different inhibitors bound to serine pro-teinases we have chosen as an illustration the binding of a small peptide inhibitor, Ac-Pro-Ala-Pro-Tyr-COOH to a bacterial chymotrypsin (Figure 11.9). The enzyme-peptide complex was formed by adding a large excess of the substrate Ac-Pro-Ala-Pro-Tyr-CO-NHz to crystals of the enzyme. The enzyme molecules within the crystals catalyze cleavage of the terminal amide group to produce the products Ac-Pro-Ala-Pro-Tyr-COOH and NHs. The ammonium ions diffuse away, but the peptide product remains bound as an inhibitor to the active site of the enzyme. 

Enantioselective oxidation of cyclic dithioacetals to monosulfoxides catalyzed by bacterial cyclohexanone monooxygenases 96CC2303. 

The biochemical mechanism of bacterial luminescence has been studied in detail and reviewed by several authors (Hastings and Nealson, 1977 Ziegler and Baldwin, 1981 Lee et al., 1991 Baldwin and Ziegler, 1992 Tu and Mager, 1995). Bacterial luciferase catalyzes the oxidation of a long-chain aldehyde and FMNH2 with molecular oxygen, thus the enzyme can be viewed as a mixed function oxidase. The main steps of the luciferase-catalyzed luminescence are shown in Fig. 2.1. Many details of this scheme have been experimentally confirmed. 

The reported quantum yields of the long-chain aldehydes in the luminescence reaction catalyzed by P. fischeri luciferase are 0.1 for dodecanal with the standard I (Lee, 1972) 0.13 for decanal with the standard I (McCapra and Hysert, 1973) and 0.15-0.16 for decanal, dodecanal and tetradecanal with the standard III (Shimomura et al., 1972). Thus, the quantum yield of long-chain aldehydes in the bacterial bioluminescence reaction appears to be in the range of 0.10-0.16. 

Three types of synthases catalyze the addition of phosphoenolpyruvate (PEP) to aldoses or the corresponding terminal phosphate esters. By concurrent release of inorganic phosphate from the preformed enolate nucleophile, the additions are essentially irreversible. None of the enzymes are yet commercially available and little data are available oil the individual specificities for the aldehydic substrates. A bacterial NeuAc synthase (EC 4.1.3.19) has been used for the microscale synthesis of A -acetylncuraminic acid from Af-acetyl-D-mannosamine31 and its 9-azido analog from 2-acetamido-6-azido-2,6-dideoxy-D-mannose32. 

An example for proteases are the (3-lactamases that hydrolyse a peptide bond in the essential (3-lactam ring of penicillins, cephalosporins, carbapenems and monobac-tams and, thereby, iireversibly inactivate the diug. 13-lactamases share this mechanism with the penicillin binding proteins (PBPs), which are essential enzymes catalyzing the biosynthesis of the bacterial cell wall. In contrast to the PBPs which irreversibly bind (3-lactams to the active site serine, the analogous complex of the diug with (3-lactamases is rapidly hydrolyzed regenerating the enzyme for inactivation of additional (3-lactam molecules. 

Bacterial as well as eukaryotic chromosomes contain too much DNA to fit easily into a cell. Therefore, the DNA must be condensed (compacted) to fit into the cell or nucleus. This is accomplished by supercoiling the DNA into a highly condensed form. When relaxed circular DNA is twisted in the direction that the helix turns, the DNA becomes positively supercoiled, if it is twisted in the opposite direction, it is called negatively supercoiled. Bacterial DNA is normally found in a negatively supercoiled state. Supercoiling reactions are catalyzed by topoisomerases. 

Hen egg-white lysozyme catalyzes the hydrolysis of various oligosaccharides, especially those of bacterial cell walls. The elucidation of the X-ray structure of this enzyme by David Phillips and co-workers (Ref. 1) provided the first glimpse of the structure of an enzyme-active site. The determination of the structure of this enzyme with trisaccharide competitive inhibitors and biochemical studies led to a detailed model for lysozyme and its hexa N-acetyl glucoseamine (hexa-NAG) substrate (Fig. 6.1). These studies identified the C-O bond between the D and E residues of the substrate as the bond which is being specifically cleaved by the enzyme and located the residues Glu 37 and Asp 52 as the major catalytic residues. The initial structural studies led to various proposals of how catalysis might take place. Here we consider these proposals and show how to examine their validity by computer modeling approaches. 

The serine proteases are the most extensively studied class of enzymes. These enzymes are characterized by the presence of a unique serine amino acid. Two major evolutionary families are presented in this class. The bacterial protease subtilisin and the trypsin family, which includes the enzymes trypsin, chymotrypsin, elastase as well as thrombin, plasmin, and others involved in a diverse range of cellular functions including digestion, blood clotting, hormone production, and complement activation. The trypsin family catalyzes the reaction ... 

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