Metal ion cofactors

Cofactors serve functions similar to those of prosthetic groups but bind in a transient, dissociable manner either to the enzyme or to a substrate such as ATP. Unlike the stably associated prosthetic groups, cofactors therefore must be present in the medium surrounding the enzyme for catalysis to occur. The most common cofactors also are metal ions. Enzymes that require a metal ion cofactor are termed metal-activated enzymes to distinguish them from the metalloenzymes for which metal ions serve as prosthetic groups. 

Enzyme pH optimal Ipl Reaction rate fccat (in vitro) [s-i] Localization Metal ion Cofactors Mw [kDa] Comments Substrates Refs. 

We next focus on the use of fixed-site cofactors and coenzymes. We note that much of this coenzyme chemistry is now linked to very local two-electron chemistry (H, CH3", CH3CO-, -NH2,0 transfer) in enzymes. Additionally, one-electron changes of coenzymes, quinones, flavins and metal ions especially in membranes are used very much in very fast intermediates of twice the one-electron switches over considerable electron transfer distances. At certain points, the chains of catalysis revert to a two-electron reaction (see Figure 5.2), and the whole complex linkage of diffusion and carriers is part of energy transduction (see also proton transfer and Williams in Further Reading). There is a variety of additional coenzymes which are fixed and which we believe came later in evolution, and there are the very important metal ion cofactors which are separately considered below. 

Enzymes may not function well or at all unless some other species known as a cofactor is present. An enzyme alone is referred to as the apoenzyme and the combination of enzyme and cofactor is known as the holoenzyme. Among the species that function as cofactors are organic compounds that interact with the enzyme. If the organic moiety is strongly attached to the enzyme, it is called a prosthetic group, but if it is loosely bound to the enzyme, it is referred to as a coenzyme. For the purposes of this discussion, the most interesting cofactors are metal ions. Depending on the type of enzyme, the appropriate metal ion cofactor may be Mg2+, Ca2+, K+, Fe2+, or Cu2+. A sizeable number of enzymes are sometimes called metalloenzymes because they have active sites that contain a metal. 

Metal ion-catalyzed hydrolytic processes have been studied for a long time, and many interesting systems have been explored which give valuable information about catalysis. However, with very few exceptions the catalysis afforded by these systems in water is disappointing when compared with enzymatic systems where a metal ion cofactor activates a substrate and a nucleophilic or basic group in an acyl or phos-phoryl transfer process. It has been noted that bulk water may not be a good medium to approximate the medium inside the active site of an enzyme where it is now known that the effective dielectric constants resemble those of organic solvents rather than water. 

A rather new approach for detecting metal ions with very high sensitivity and selectivity utilizes DNAzymes. DNAzymes are a special class of enzymes formed from DNA nucleotides. Compared to proteins and ribozymes, they are more stable, structurally simpler, and therefore cheaper. As DNAzymes often require metal ion cofactors, they are interesting sensing platforms for these metal ions [149]. 

The importance of the biochemistry of hydration of CO2 and dehydration of HCOg in an aqueous environment has led to extensive and invigorating research on the enzyme carbonic anhydrase pertaining to its structural details, metal ion cofactor, its coordination environment (12) and kinetic activity Model studies, both theoretical and experimental, have been undertaken using primarily the complexes of Zn(II), Mn(II), and Co(II), the latter one being its closest equivalent (13). 

The antitumor antibiotic bleomycin (BLM) is believed to cause cytotoxicity through its ability, in the combined presence of dioxygen and a metal ion cofactor (204), to bind to and degrade DNA (205). Iron complexes of BLM have aroused special attention, as such complexes are the first (vide supra concerning the discussion of hemerythrin and hemocyanin) non-heme-iron complexes with a significant capacity for dioxygen activation (206). 

What substances are required (substrate, metal ions, cofactors, etc.) and... 

An enzyme cofactor can be either an inorganic ion (usually a metal cation) or a small organic molecule called a coenzyme. In fact, the requirement of many enzymes for metal-ion cofactors is the main reason behind our dietary need for trace minerals. Iron, zinc, copper, manganese, molybdenum, cobalt, nickel, and selenium are all essential trace elements that function as enzyme cofactors. A large number of different organic molecules also serve as coenzymes. Often, although not always, the coenzyme is a vitamin. Thiamine (vitamin Bj), for example, is a coenzyme required in the metabolism of carbohydrates. 

For 3 —51 RNA ligation using the 2/,3/-cyclic phosphate substrate combination of Fig. 5.2A, a suitable combination of selection design aspects (including use of Zn2+ as the metal ion cofactor) leads to the desired native linkages (Kost et al, 2008). However, as is the case for the 57-triphosphate substrate combination, a selection pressure for sequence generality must again be imposed to identify useful deoxyribozymes. 

When the metal ion cofactor is electroactive at potentials equal or more positive than that for the one-electron reduction of 02, then an elfective two-electron reduction is accomplished by two sequential one-electron reductions [see Eq. (9.61)]. Such a process is similar to the favored 02-activation mechanism for cytochrome P-450.40... 

Many enzymes require metal ion cofactors for their activity. Such enzymes are either metalloenzymes, in which case the metal ion is tightly bound, or metal-activated enzymes, in which case the bound metal ion is retained in an equilibrium with free metal ions. 

Naturally occurring and synthetic ribozymes often require metal ion cofactors 2+... 

However, not all cleavage reactions of nucleic acids promoted by metal ions occur through direct involvement of metal ions in cleavage chemistry. For example, metal ion cofactors stabihze the catalytically active conformations of several ribozymes, but do not participate directly in catalysis. ... 

The hepatitis delta virus (HDV) ribozyme is a member of the class of small ribozymes and functions as a self-cleaving RNA sequence critical to the replication of the virus RNA genome (1, 8, 40). HDV ribozymes are proposed to employ several catalytic strategies that include an important example of general acid/base catalysis that involves a specific cytosine residue in the active site. Indeed, a milestone in our understanding of RNA catalysis was the observation that HDV and other small ribozymes could function in the absence of divalent metal ion cofactors, provided that high (molar) concentrations of monovalent ions are present (41, 42). These high monovalent ion concentrations are believed to stabilize the active RNA conformation, which implies that the primary role of divalent metal ions is in structural stabilization (42). 

X 10 p,M s with Mn " " as a cofactor. These very low efficiencies are common to several sesquiterpene synthases but substantial differences have been reported. The synthase reached a kcatK value of 9.7 x 10 p,M s for conversion of FPP at pH 9.5 using Mg + as a metal ion cofactor. This increase in efficiency is interesting and shows the broad window in which the enzyme... 

These chelating resins have found most of their use in metal ion recovery processes in the chemical and waste recovery industries. They may find use in fermentation applications where the cultured organism requires the use of metal ion cofactors. Specific ion exchange resins have also been used in laboratory applications that may find eventual use in biotechnology product recovery applications. 

The chemical potential of side chains found in amino acids is limited for example, there are no efficient electron acceptors. Therefore, enzyme catalysis incorporates if necessary additional chemical potential by specific metal ions, for example, Zn2+ (see Fig. 1-6), Fe2+ Co2+, Cu2+ and others Examples are shown in Fig. 1-8 for the coordination of the transition metal ions in protein structures. Besides metal ions, cofactors or coenzymes serve to activate groups and participate in the catalytic process. A summary of cofactors and coenzymes is given in Table 1-4 the relation to vitamins is quite apparent. Chemical structures are presented in Table 1-5. Coenzymes and cofactors may act by nucleophilic or electrophilic attack on the sub-... 

The enzyme is a homodimeric protein of A/r 170,000 and contains no known organic or metal ion cofactors. The enzyme is readily inactivated by oxygen and interconverts between active and inactive forms in vivo (173, 174). The activation process occurs under conditions of anaerobiosis and is catalyzed by an Fe(ll)-dependent activating enzyme (Mr 30,000) (775). Elegant studies on the in vitro activation of PFL by Knappe and co-workers (176, 177) have revealed that a complex activation cocktail is required, which includes the activating enzyme, pyruvate, or oxamate as allosteric effectors, S-adenosylmethionine (SAM), and flavodoxin (775) or photoreduced 5-deazariboflavin (178). A possible role for a B12 derivative in the activation or catalytic reaction for PFL is not likely in light of the observation that E. coli 113-3, a methionine/B auxotroph, pos-... 

Coenzymes are small organic molecules that link to enzymes and whose presence is essential to the activity of those enzymes. Coenzymes belong to the larger group called cofactors, which also includes metal ions cofactor is the more general term for small molecnles reqnired for the activity of their associated enzymes. The relationship between these two terms is as follows... 

This would be analogous to the change that results from alkyl substitution that is, transition states become more associative in the continuum from monoesters to triesters. Although relatively few phosphatases have been subjected to serious scrutiny of their transition states, in the cases that have been reported, this prediction has not been borne out. The reactions catalyzed by AP proceeds through loose transition states that are not significantly altered from those in solution, both in its phosphatase and in its promiscuous sulfatase activities. " Results with A-phosphatase and with calcineurin, which both catalyze phosphoryl transfer to a metal-coordinated hydroxide nucleophile, also provide no evidence of a significantly different transition state. Protein tyrosine phosphatases (PTPs), which do not contain metal ion cofactors but have a conserved arginine residue and proceed via a phosphocysteine intermediate, similarly catalyze phosphoryl transfer via a transition state similar to the one in solution. ... 

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