Metallo Enzymes

Metalloenzymes

Metalloenzymes are enzyme-containing metal ions, which are directly bound to the protein or enzyme-bound nonprotein components (prosthetic groups). The metal ion being cofactors aids the overall enzymatic activity. One staggering fact is that about one-third of all enzymes we know are metalloenzymes. All Metalloenzymes have one common feature, namely that the metal ion is bound to the protein at one labile coordination site. It is essential to know the shape of the active site for enzymatic activity and the metal ion is in a pocket whose shape fits the substrate. Ribozyme They are unique because they are made of ribonucleic acid (RNA) unlike other enzymes. They are found in the organelles of plants, lower eukaryotes, prokaryotes, bacteriophages, viroids and satellite viruses that infect plants. Ribozymes have been transformed, with intelligent engineering, into RNA enzymes that can cleave or modify targeted RNAs (or even DNAs) without altering themselves. The general mechanism appears to use a general acid-base for catalysis. Magnesium, or other divalent metal ions, are primarily used to stabilize the tertiary structures of these ribozymes. Being the most abundant divalent metal Mg2+ is used also because it has a high affinity for the negatively charged phosphate backbone of RNA. The double positive charge allows bridging of two phosphates from distant RNA regions, enabling a long-range structure formation. Ribozymes can form intricate three-dimensional structures that challenge the complexity of protein made enzymes, allowing for the precise positioning of the substrate in the catalytic core. Additionally, Mg2+ in aqueous solution is able to form the deprotonated Mg(OH)(aq)+ complex that, due to its residual positive charge, can still binds to RNA. First impressions, the four nucleobases of RNA (cytosine, uracil, guanine, adenine,) seemed quite less compared to twenty bases in Amino acids. A properly positioned Mg(OH)(aq)+ ion, acts as a base catalyst, could easily be intended as an essential cofactor for most of the chemical reactions. For this reason, ribozymes were no more thought as chemically inferior to proteins, Several auto-splicing or auto-cleaving RNAs were identified that make single cuts in precisely laid out RNA sequences Although the reactions are often facilitated by protein cofactors in vivo, the active enzyme in each case is the RNA component. Two general mechanisms are recognized for splicing and cleavage reactions differing in only a few steps. ⮚ Larger ribozymes can not only accurately position an RNA substrate in a pre-organized active site, but it can also position a second substrate in the same way such as a nucleoside to react it with as a nucleophile. Thus, RNA can drive catalysis by forced proximity of reaction partners. ⮚ A second learning is the fact that ribozymes have found paths to use their own side chains directly to do the chemistry. Two examples from small catalytic RNAs, hepatitis delta virus (HDV) and the hairpin ribozymes. In both cases, the ribozyme accurately fixes the location of its substrate by hydrogen bonding in a specific binding pocket. The human analogy to explain this is that of a capable blacksmith, holding his me to the anvil to ply it with his hammer in a certain spot. No wonder why that Ribozymes are so precise and adept. (According to the figure) The red nucleotides are poised to act on the substrate by abstracting or donating a proton. Dashed purple tubes, hydrogen bonds to fix the substrate in place.) Uses of Ribozymes A Ribozyme is a unit functioning under the large subunit ribosomal RNA to connect amino acids during protein production. They are also a part of a variety of RNA processing reactions, including viral replication, RNA splicing and transfer RNA biosynthesis. Ribozymes have been suggested and developed for curing a disease through gene therapy. One significant difficulty in using RNA based enzymes as a therapeutic is the short half-life of the catalytic RNA molecules in the body. This problem was overcome the 2’ position on the ribose is altered to improve RNA stability. One other field of ribozyme gene therapy has been the inhibition of RNA-based viruses. A type of synthetic ribozyme has been developed, which is directed against HIV RNA called gene shears and has entered clinical testing for HIV infection. Zinc Metalloenzymes Zinc is an essential requirement for the activity of nearly 300 enzymes under the umbrella of six classes of enzymes (Transferases, Hydrolases, Oxidoreductases, Lyases, Isomerases, and Ligases.). Several properties relate to their biological usability and versatility. Its amphoteric nature allows the zinc-coordinated water to exist as a hydroxide ion or hydronium (rarely) even at neutrality. Its coordination sphere is flexible attaches to a wide variety of ligands, allowing for a multiplicity of types and numbers of coordination complex geometries. Its stable d-shell signifies that it is neither oxidized or reduced; yet it is involved in - oxidoreductive enzymatic reactions in coordination with an organic cofactor. The zinc-bound water is the major component of the active site; it is activated for enzymatic breakdown by identifying and arranging the ligands coordinated to zinc. Thus, ultimately, it is this water molecule which, upon entering the zinc coordination sphere, is activated either by ionization, polarization or displacement. Zinc in proteins can either participate directly in chemical catalysis or be important for maintaining protein structure and stability. Overall, in all catalytic sites, the zinc ion functions as a Lewis acid. In multi-metal containing enzymes, the two or more zinc (or even other metal) atoms may operate in concert to enhance catalysis. A class of catalytic zinc sites, called Cocatalytic zinc sites, has been defined in which two or more zinc atoms are close to one another. Uses of Zinc Zinc metalloenzymes participate in a vast number of metabolic processes including carbohydrate, lipid, protein and nucleic acid synthesis, regulation and degradation. Zinc is part of carbonate dehydratase , activates enzymes of protein metabolism and carbon dioxide transfer, and is important for normal immune functioning of the body. While spontaneous zinc deficiency is not common, experimental deficiency causes alopecia and dermal lesions on the extremities. Example of some of the most useful zinc metalloenzymes include ⮚ Insulin-degrading enzyme -Can destroy amyloid beta (Aβ), a peptide involved in the pathogenesis of Alzheimer's disease. ⮚ Alcohol dehydrogenase – Present abundantly in liver, inner lining of stomach. It catalyzes the oxidation of ethanol to acetaldehyde: ⮚ Zinc carboxypeptidase- Secreted by the pancreas secreted into the small intestine and is used to speed up this hydrolysis reaction. These are just some of the few examples out of the nearly 300 metalloenzymes containing Zinc as their central metal ion.