1QBJ , 1QGP , 1XMK , 2ACJ , 2GXB , 2L54 , 2MDR , 3F21 , 3F22 , 3F23 , 3IRQ , 3IRR
112-466: 103 56417 ENSG00000160710 ENSMUSG00000027951 P55265 Q99MU3 NM_001365045 NM_001365046 NM_001365047 NM_001365048 NM_001365049 NM_001038587 NM_001146296 NM_019655 NM_001357958 NP_001020278 NP_001102 NP_001180424 NP_056655 NP_056656 NP_001033676 NP_001139768 NP_062629 NP_001344887 The double-stranded RNA-specific adenosine deaminase enzyme family are encoded by
224-487: A catalytic triad , stabilize charge build-up on the transition states using an oxyanion hole , complete hydrolysis using an oriented water substrate. Enzymes are not rigid, static structures; instead they have complex internal dynamic motions – that is, movements of parts of the enzyme's structure such as individual amino acid residues, groups of residues forming a protein loop or unit of secondary structure , or even an entire protein domain . These motions give rise to
336-489: A conformational ensemble of slightly different structures that interconvert with one another at equilibrium . Different states within this ensemble may be associated with different aspects of an enzyme's function. For example, different conformations of the enzyme dihydrofolate reductase are associated with the substrate binding, catalysis, cofactor release, and product release steps of the catalytic cycle, consistent with catalytic resonance theory . Substrate presentation
448-467: A zinc ion. The zinc activates the water molecule for the nucleophilic hydrolytic deamination. Within the catalytic core there is an inositol hexakisphosphate (IP6), which stabilizes arginine and lysine residues. [REDACTED] In mammals the conversion from A to I requires homodimerization of ADAR1 and ADAR2, but not ADAR3. In vivo studies have are not conclusive if RNA binding is required for dimerization. A study with ADAR family mutants showed
560-511: A catalyst in a reaction. Both forms also have similar expression pattern structures of proteins and require substrate double-stranded RNA structures. However, they differ in their editing activity in that both ADAR one and two can edit GluR-B pre-mRNA at the R/G site and only ADAR2 can alter the Q/R site. ADAR1 has been found two have two isoforms, ADAR1p150 and ADARp110. ADAR1p110 is typically found in
672-523: A cell-free environment which allows easier manipulation. The first vertebrate ever to be cloned was an African clawed frog in 1962, an experiment for which Sir John Gurdon was awarded the Nobel Prize in Physiology or Medicine in 2012 "for the discovery that mature cells can be reprogrammed to become pluripotent". Additionally, four female African clawed frogs and stored sperm were present on
784-429: A critical protein present in all eukaryotes , early in the metazoan period through the addition of a dsRNA binding domain . This likely occurred in the lineage which leads to the crown Metazoa. When a duplicate ADAT gene was coupled to another gene which encoded at least one double stranded RNA binding. The ADAR family of genes has been largely conserved over the history of its existence. This, along with its presence in
896-432: A developmentally regulated activity that denatures RNA:RNA hybrids in embryos. In 1988, Richard Wagner et al. further studied the activity occurring on Xenopus embryos. They determined a protein was responsible for unwinding of RNA due to the absence of activity after proteinase treatment. This protein is specific for dsRNA and does not require ATP . It became evident this protein's activity on dsRNA modifies it beyond
1008-548: A few. Research on measles virus shows ADAR1 enhancing viral replication through two different mechanisms: RNA editing and inhibition of dsRNA-activated protein kinase ( PKR ). Specifically, viruses are thought to use ADAR1 as a positive replication factor by selectively suppressing dsRNA-dependent and antiviral pathways. Enzyme Enzymes ( / ˈ ɛ n z aɪ m z / ) are proteins that act as biological catalysts by accelerating chemical reactions . The molecules upon which enzymes may act are called substrates , and
1120-477: A first step and then checks that the product is correct in a second step. This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases. Similar proofreading mechanisms are also found in RNA polymerase , aminoacyl tRNA synthetases and ribosomes . Conversely, some enzymes display enzyme promiscuity , having broad specificity and acting on
1232-459: A harmful invasive species. They can travel short distances to other bodies of water, and some have even been documented to survive mild freezes. They have been shown to devastate native populations of frogs and other creatures by eating their young. In 2003, Xenopus laevis frogs were discovered in a pond at San Francisco 's Golden Gate Park . Much debate now exists in the area on how to exterminate these creatures and keep them from spreading. It
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#17327977722601344-475: A hyobranchial pump to draw or suck things in their mouth. Pipidae have powerful legs for swimming and lunging after food. They also use the claws on their feet to tear pieces of large food. They have no external eardrums, but instead subcutaneous cartilaginous disks that serve the same function. They use their sensitive fingers and sense of smell to find food. Pipidae are scavengers and will eat almost anything living, dying, or dead and any type of organic waste. It
1456-400: A key role in the development of Xenopus laevis embryos . Previous research on Xenopus oocytes was successful. However, when Bass and Weintraub applied identical protocols to Xenopus embryos, they were unable to determine the embryo's developmental genes. To understand why the method was unsuccessful, they began comparing duplex RNA in both oocytes and embryos. This led them to discover
1568-468: A linkage between RNA-editing and nervous system disorders such as amyotrophic lateral sclerosis (ALS). Atypical RNA editing linked to ADAR may also correlate to mental disorders such as schizophrenia, epilepsy, and suicidal depression. The ADAR enzyme and its associated gene were discovered accidentally in 1987 as a result of research by Brenda Bass and Harold Weintraub . These researchers were using antisense RNA inhibition to determine which genes play
1680-541: A more comprehensive discussion of the use of these frogs in biomedical research, see Xenopus . Xenopus laevis is also notable for its use in the first widely used method of pregnancy testing . In the 1930s, two South African researchers, Hillel Shapiro and Harry Zwarenstein, students of Lancelot Hogben at the University of Cape Town , discovered that the urine from pregnant women would induce oocyte production in X. laevis within 8–12 hours of injection. This
1792-458: A more pronounced cloaca and have hip-like bulges above their rear legs where their eggs are internally located. Both males and females have a cloaca , which is a chamber through which digestive and urinary wastes pass and through which the reproductive systems also empty. The cloaca empties by way of the vent which in reptiles and amphibians is a single opening for all three systems. African clawed frogs are fully aquatic and will rarely leave
1904-490: A pathogen or virus), able to assist in a cell's immune pathway. Evidence shows elimination of HCV replicon, Lymphocytic choriomeningitis LCMV , and polyomavirus . ADAR1 is proviral in other circumstances. ADAR1’s A to I editing has been found in many viruses including measles virus, influenza virus, lymphocytic choriomeningitis virus, polyomavirus, hepatitis delta virus, and hepatitis C virus. Although ADAR1 has been seen in other viruses, it has only been studied extensively in
2016-631: A permit in the following US states: Arizona, California, Kentucky, Louisiana, New Jersey, North Carolina, Oregon, Vermont, Virginia, Hawaii, Nevada, and Washington state. However, it is legal to own Xenopus laevis in New Brunswick (Canada) and Ohio. Feral colonies of Xenopus laevis exist in South Wales , United Kingdom . In Yunnan , China there is a population of albino clawed frogs in Lake Kunming , along with another invasive:
2128-426: A point of rehybridization but does not fully denature it. Finally, the researchers determined this unwinding is due to the deamination of adenosine residues to inosine . This modification results in mismatched base-pairing between inosine and uridine , leading to the destabilization and unwinding of dsRNA. ADARs are one of the most common forms of RNA editing, and have both selective and non-selective activity. ADAR
2240-399: A possible prognostic marker. Studies have indicated that loss of ADAR1 contributes to melanoma growth and metastasis. ADAR enzymes can act on microRNA and affect its biogenesis, stability and/or its binding target. ADAR1 may be downregulated by cAMP- response element binding protein (CREB), limiting its ability to act on miRNA. One such example is miR-455-5p which is edited by ADAR1. When ADAR
2352-464: A quantitative theory of enzyme kinetics, which is referred to as Michaelis–Menten kinetics . The major contribution of Michaelis and Menten was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis–Menten complex in their honor. The enzyme then catalyzes the chemical step in
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#17327977722602464-439: A range of different physiologically relevant substrates. Many enzymes possess small side activities which arose fortuitously (i.e. neutrally ), which may be the starting point for the evolutionary selection of a new function. To explain the observed specificity of enzymes, in 1894 Emil Fischer proposed that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This
2576-451: A species' normal level; as a result, enzymes from bacteria living in volcanic environments such as hot springs are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate. Enzymes are usually much larger than their substrates. Sizes range from just 62 amino acid residues, for the monomer of 4-oxalocrotonate tautomerase , to over 2,500 residues in
2688-449: A steady level inside the cell. For example, NADPH is regenerated through the pentose phosphate pathway and S -adenosylmethionine by methionine adenosyltransferase . This continuous regeneration means that small amounts of coenzymes can be used very intensively. For example, the human body turns over its own weight in ATP each day. As with all catalysts, enzymes do not alter the position of
2800-442: A thermodynamically unfavourable one so that the combined energy of the products is lower than the substrates. For example, the hydrolysis of ATP is often used to drive other chemical reactions. Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are commonly obtained from enzyme assays . In 1913 Leonor Michaelis and Maud Leonora Menten proposed
2912-569: Is considered an invasive species in several countries , including across Europe. These frogs are plentiful in ponds and rivers within the south-eastern portion of Sub-Saharan Africa. They are aquatic and are often a mottled greenish-grey-brown in color, sometimes with yellowish botches, and with a pale white-cream belly. African clawed frogs have been frequently sold as pets, and are sometimes misidentified as African dwarf frogs . Albino clawed frogs are common and sold as animals for laboratories . Amphibians reproduce by fertilizing eggs outside of
3024-457: Is k cat , also called the turnover number , which is the number of substrate molecules handled by one active site per second. The efficiency of an enzyme can be expressed in terms of k cat / K m . This is also called the specificity constant and incorporates the rate constants for all steps in the reaction up to and including the first irreversible step. Because the specificity constant reflects both affinity and catalytic ability, it
3136-838: Is orotidine 5'-phosphate decarboxylase , which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH , and many enzymes are (permanently) denatured when exposed to excessive heat, losing their structure and catalytic properties. Some enzymes are used commercially, for example, in
3248-421: Is a process where the enzyme is sequestered away from its substrate. Enzymes can be sequestered to the plasma membrane away from a substrate in the nucleus or cytosol. Or within the membrane, an enzyme can be sequestered into lipid rafts away from its substrate in the disordered region. When the enzyme is released it mixes with its substrate. Alternatively, the enzyme can be sequestered near its substrate to activate
3360-561: Is able to fit into their mouths. Being aquatic, clawed frogs use their sense of smell and their lateral line to detect prey rather than eyesight like other frogs. However, clawed frogs can still see using their eyes and will stalk prey or watch predators by sticking their heads out of the water. Clawed frogs will dig through substrate to unearth worms and other food. Unlike other frogs, they have no tongue to extend to catch food, so clawed frogs use their hands to grab food and shovel it into their mouths. These frogs are particularly cannibalistic;
3472-405: Is able to modify and regulate the output of gene product, as inosine is interpreted by the cell to be guanosine . ADAR can change the functionality of small RNA molecules. Recently, ADARs have also been discovered as a regulator on splicing and circRNA biogenesis with their editing capability or RNA binding function. It is believed that ADAR evolved from ADAT (Adenosine Deaminase Acting on tRNA),
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3584-431: Is caused by incorrect activation of interferon inducible genes such as those activated to fight off viral infections. Mutation and loss of function of ADAR1 prevents destabilization of double stranded RNA (dsRNA). This buildup of dsRNA stimulates IFN production without a viral infection, causing an inflammatory reaction and autoimmune response. The phenotype in the knock-out mice is rescued by the p150 form of ADAR1 containing
3696-632: Is considered a more viable model for genetics, although gene editing protocols have now been perfected for. Roger Wolcott Sperry used X. laevis for his famous experiments describing the development of the visual system. These experiments led to the formulation of the chemoaffinity hypothesis . X. laevis have been used as a model organism in vertebrae cardiogenesis, human congenital heart defects, and in GWAS studies of congenital heart defects. Xenopus oocytes provide an important expression system for molecular biology . By injecting DNA or mRNA into
3808-437: Is described by "EC" followed by a sequence of four numbers which represent the hierarchy of enzymatic activity (from very general to very specific). That is, the first number broadly classifies the enzyme based on its mechanism while the other digits add more and more specificity. The top-level classification is: These sections are subdivided by other features such as the substrate, products, and chemical mechanism . An enzyme
3920-541: Is downregulated by CREB the unedited miR-455-5p downregulates a tumor suppressor protein called CPEB1, contributing to melanoma progression in an in vivo model. A Gly1007Arg mutation in ADAR1, as well as other truncated versions, have been implicated as a cause in some cases of DSH1. This is a disease characterized by hyperpigmentation in the hands and feet and can occur in Japanese and Chinese families. Expression levels of
4032-749: Is fully specified by four numerical designations. For example, hexokinase (EC 2.7.1.1) is a transferase (EC 2) that adds a phosphate group (EC 2.7) to a hexose sugar, a molecule containing an alcohol group (EC 2.7.1). Sequence similarity . EC categories do not reflect sequence similarity. For instance, two ligases of the same EC number that catalyze exactly the same reaction can have completely different sequences. Independent of their function, enzymes, like any other proteins, have been classified by their sequence similarity into numerous families. These families have been documented in dozens of different protein and protein family databases such as Pfam . Non-homologous isofunctional enzymes . Unrelated enzymes that have
4144-476: Is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase . Examples are lactase , alcohol dehydrogenase and DNA polymerase . Different enzymes that catalyze the same chemical reaction are called isozymes . The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers (for "Enzyme Commission") . Each enzyme
4256-418: Is often referred to as "the lock and key" model. This early model explains enzyme specificity, but fails to explain the stabilization of the transition state that enzymes achieve. In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continuously reshaped by interactions with the substrate as the substrate interacts with
4368-462: Is only one of several important kinetic parameters. The amount of substrate needed to achieve a given rate of reaction is also important. This is given by the Michaelis–Menten constant ( K m ), which is the substrate concentration required for an enzyme to reach one-half its maximum reaction rate; generally, each enzyme has a characteristic K M for a given substrate. Another useful constant
4480-404: Is seen. This is shown in the saturation curve on the right. Saturation happens because, as substrate concentration increases, more and more of the free enzyme is converted into the substrate-bound ES complex. At the maximum reaction rate ( V max ) of the enzyme, all the enzyme active sites are bound to substrate, and the amount of ES complex is the same as the total amount of enzyme. V max
4592-403: Is the ribosome which is a complex of protein and catalytic RNA components. Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what substrates they bind and then the chemical reaction catalysed. Specificity is achieved by binding pockets with complementary shape, charge and hydrophilic / hydrophobic characteristics to
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4704-441: Is their primary role is to increase the diversity of transcripts and expand the protein variation, promoting evolution of proteins. In mammals, there are three types of ADAR enzymes: ADAR (ADAR1), ADARB1 (ADAR2), and ADARB2 (ADAR3). ADAR (ADAR1) and ADAR2 (ADARB1) ADAR one and two are both found within various tissues of the body. These two forms of ADAR are also found to be catalytically active, meaning they can be used as
4816-486: Is unknown if these frogs entered the San Francisco ecosystem through intentional release or escape into the wild. San Francisco officials drained Lily Pond and fenced off the area to prevent the frogs from escaping to other ponds in the hopes they starve to death. Due to incidents in which these frogs were released and allowed to escape into the wild, African clawed frogs are illegal to own, transport or sell without
4928-790: Is useful for comparing different enzymes against each other, or the same enzyme with different substrates. The theoretical maximum for the specificity constant is called the diffusion limit and is about 10 to 10 (M s ). At this point every collision of the enzyme with its substrate will result in catalysis, and the rate of product formation is not limited by the reaction rate but by the diffusion rate. Enzymes with this property are called catalytically perfect or kinetically perfect . Example of such enzymes are triose-phosphate isomerase , carbonic anhydrase , acetylcholinesterase , catalase , fumarase , β-lactamase , and superoxide dismutase . The turnover of such enzymes can reach several million reactions per second. But most enzymes are far from perfect:
5040-529: The ADAR family genes . ADAR stands for adenosine deaminase acting on RNA . This article focuses on the ADAR proteins; This article details the evolutionary history, structure, function, mechanisms and importance of all proteins within this family. ADAR enzymes bind to double-stranded RNA (dsRNA) and convert adenosine to inosine ( hypoxanthine ) by deamination . ADAR proteins act post-transcriptionally, changing
5152-486: The American bullfrog . Because this population is albino, it suggests that the clawed frogs originated from the pet trade or a laboratory. The African clawed frog may be an important vector and the initial source of Batrachochytrium dendrobatidis , a chytrid fungus that has been implicated in the drastic decline in amphibian populations in many parts of the world. Unlike in many other amphibian species (including
5264-614: The DNA polymerases ; here the holoenzyme is the complete complex containing all the subunits needed for activity. Coenzymes are small organic molecules that can be loosely or tightly bound to an enzyme. Coenzymes transport chemical groups from one enzyme to another. Examples include NADH , NADPH and adenosine triphosphate (ATP). Some coenzymes, such as flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), thiamine pyrophosphate (TPP), and tetrahydrofolate (THF), are derived from vitamins . These coenzymes cannot be synthesized by
5376-476: The Space Shuttle Endeavour when it was launched into space on mission STS-47 on September 12, 1992, so that scientists could test whether reproduction and development could occur normally in zero gravity. Xenopus laevis also serves as an ideal model system for the study of the mechanisms of apoptosis. In fact, iodine and thyroxine stimulate the spectacular apoptosis of the cells of
5488-511: The law of mass action , which is derived from the assumptions of free diffusion and thermodynamically driven random collision. Many biochemical or cellular processes deviate significantly from these conditions, because of macromolecular crowding and constrained molecular movement. More recent, complex extensions of the model attempt to correct for these effects. Enzyme reaction rates can be decreased by various types of enzyme inhibitors. A competitive inhibitor and substrate cannot bind to
5600-717: The mediobasal hypothalamus , then it stimulates seasonal testicular growth; if peripherally, then testicular regression and cold-season thermogenesis. These observations are regarded as widely applicable across vertebrate thyroid systems. The lipidomics of Xenopus oocytes have been studied by Tian et al 2014 and Phan et al 2015. In X. laevis , epigenetic methylation changes in neural-developmental genes associated with aging are analogous to aging related epigenetic changes in mammalian species. This finding suggests that, during their evolutionary divergence, patterns of epigenetic changes in neural-development genes during aging have been conserved between frogs and mammals C. In
5712-500: The nucleotide content of RNA. The conversion from adenosine to inosine (A to I) in the RNA disrupts the normal A:U pairing, destabilizing the RNA. Inosine is structurally similar to guanine (G) which leads to inosine to cytosine (I:C) binding. Inosine typically mimics guanosine during translation but can also bind to uracil, cytosine, and adenosine, though it is not favored. Codon changes may arise from RNA editing leading to changes in
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#17327977722605824-481: The oocyte . Translation of proteins can be blocked or splicing of pre-mRNA can be modified by injection of Morpholino antisense oligos into the oocyte (for distribution throughout the embryo) or early embryo (for distribution only into daughter cells of the injected cell). Extracts from the eggs of X. laevis frogs are also commonly used for biochemical studies of DNA replication and repair, as these extracts fully support DNA replication and other related processes in
5936-461: The ADAR1 protein have shown to be elevated during HIV infection and it has been suggested that it is responsible for A to G mutations in the HIV genome, inhibiting replication. The mutation in the HIV genome by ADAR1 might in some cases lead to beneficial viral mutations which could contribute to drug resistance. ADAR1 is an interferon ( IFN )-inducible protein (one released by a cell in response to
6048-568: The National Institutes of Health. The work rapidly expanded to include de novo reconstruction of X. laevis transcripts, in collaboration with groups around the world donating Illumina Hi-Seq RNA sequencing datasets. Genome sequencing by the Rokhsar and Harland groups (UC Berkeley) and by Taira and collaborators (University of Tokyo, Japan) gave a major boost to the project, which, with additional contributions from investigators in
6160-496: The Netherlands, Korea, Canada and Australia, led to publication of the genome sequence and its characterization in 2016. X. laevis oocytes are often used as an easy model for the artificially induced expression of transgenes . For example, they are commonly used when studying chloroquine resistance produced by specialized transporter mutants. Even so the foreign expression tissue may itself confer some alterations to
6272-676: The Zα domain that binds specifically to the left-handed double-stranded conformation found in Z-DNA and Z-RNA, but not by the p110 isoform lacking this domain. In humans, the P193A mutation in the Zα domain is causal for Aicardi–Goutières syndrome and for the more severe phenotype found in Bilateral Striatal Necrosis/Dystonia. The findings establish a biological role for the left-handed Z-DNA conformation. In motor neurons,
6384-400: The ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules , also called ribozymes . They are sometimes described as a type of enzyme rather than being like an enzyme, but even in
6496-437: The active site and are involved in catalysis. For example, flavin and heme cofactors are often involved in redox reactions. Enzymes that require a cofactor but do not have one bound are called apoenzymes or apoproteins . An enzyme together with the cofactor(s) required for activity is called a holoenzyme (or haloenzyme). The term holoenzyme can also be applied to enzymes that contain multiple protein subunits, such as
6608-502: The active site. Organic cofactors can be either coenzymes , which are released from the enzyme's active site during the reaction, or prosthetic groups , which are tightly bound to an enzyme. Organic prosthetic groups can be covalently bound (e.g., biotin in enzymes such as pyruvate carboxylase ). An example of an enzyme that contains a cofactor is carbonic anhydrase , which uses a zinc cofactor bound as part of its active site. These tightly bound ions or molecules are usually found in
6720-407: The animal fatty acid synthase . Only a small portion of their structure (around 2–4 amino acids) is directly involved in catalysis: the catalytic site. This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and binding site together compose the enzyme's active site . The remaining majority of the enzyme structure serves to maintain
6832-578: The average values of k c a t / K m {\displaystyle k_{\rm {cat}}/K_{\rm {m}}} and k c a t {\displaystyle k_{\rm {cat}}} are about 10 5 s − 1 M − 1 {\displaystyle 10^{5}{\rm {s}}^{-1}{\rm {M}}^{-1}} and 10 s − 1 {\displaystyle 10{\rm {s}}^{-1}} , respectively. Michaelis–Menten kinetics relies on
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#17327977722606944-619: The beginning and terminating regions of translation. However, crucial amino acid changes can occur, resulting in change of function of several cellular processes. Amino acid changes can result in protein structural changes at secondary, tertiary, and quaternary structures. Researchers observed high levels of oncogenetic A-to-I editing in circular RNA precursors, directly confirming ADAR's relationship to cancer. A list of tumor related RNA editing sites can be found here . Studies of patients with hepatocellular carcinoma (HCC) have shown trends of upregulated ADAR1 and downregulated ADAR2. Results suggest
7056-502: The body de novo and closely related compounds (vitamins) must be acquired from the diet. The chemical groups carried include: Since coenzymes are chemically changed as a consequence of enzyme action, it is useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes. For example, about 1000 enzymes are known to use the coenzyme NADH. Coenzymes are usually continuously regenerated and their concentrations maintained at
7168-471: The chemical equilibrium of the reaction. In the presence of an enzyme, the reaction runs in the same direction as it would without the enzyme, just more quickly. For example, carbonic anhydrase catalyzes its reaction in either direction depending on the concentration of its reactants: The rate of a reaction is dependent on the activation energy needed to form the transition state which then decays into products. Enzymes increase reaction rates by lowering
7280-518: The clawed frogs can burrow themselves into the mud, becoming dormant for up to a year. Xenopus laevis have been known to survive 15 or more years in the wild and 25–30 years in captivity. They shed their skin every season, and eat their own shed skin. Although lacking a vocal sac , the males make a mating call of alternating long and short trills, by contracting the intrinsic laryngeal muscles . Females also answer vocally, signaling either acceptance (a rapping sound) or rejection (slow ticking) of
7392-514: The closely related western clawed frog ) where this chytrid fungus causes the disease Chytridiomycosis , it does not appear to affect the African clawed frog, making it an effective carrier. Invasive: The African clawed frog is considered invasive by the Centre of Invasive biology from Stellenbosh University with this species even going as far as predating on other species. There has even been
7504-534: The coding sequences for proteins and their functions. Most editing sites are found in noncoding regions of RNA such as untranslated regions (UTRs), Alu elements , and long interspersed nuclear elements (LINEs). Codon changes can give rise to alternate transcriptional splice variants. ADAR impacts the transcriptome in editing-independent ways, likely by interfering with other RNA-binding proteins. Mutations in this gene are associated with several diseases including HIV, measles, and melanoma. Recent research supports
7616-425: The conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified. French chemist Anselme Payen was the first to discover an enzyme, diastase , in 1833. A few decades later, when studying the fermentation of sugar to alcohol by yeast , Louis Pasteur concluded that this fermentation was caused by a vital force contained within
7728-444: The decades since ribozymes' discovery in 1980–1982, the word enzyme alone often means the protein type specifically (as is used in this article). An enzyme's specificity comes from its unique three-dimensional structure . Like all catalysts, enzymes increase the reaction rate by lowering its activation energy . Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example
7840-431: The dsRBD there is a conserved α-β-β-β-α configuration. ADAR1 contains two areas for binding Z-DNA known as Zα and Zβ. ADAR2 and ADAR3 have an arginine rich single stranded RNA (ssRNA) binding domain. A crystal structure of ADAR2 has been solved. In the enzyme active site, there is a glutamic acid residue(E396) that hydrogen bonds to a water. A histidine (H394) and two cysteine residues (C451 and C516) coordinate with
7952-433: The energy of the transition state. First, binding forms a low energy enzyme-substrate complex (ES). Second, the enzyme stabilises the transition state such that it requires less energy to achieve compared to the uncatalyzed reaction (ES ). Finally the enzyme-product complex (EP) dissociates to release the products. Enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive"
8064-592: The enzyme urease was a pure protein and crystallized it; he did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley , who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin . These three scientists were awarded the 1946 Nobel Prize in Chemistry. The discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography . This
8176-483: The enzyme at the same time. Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example, the drug methotrexate is a competitive inhibitor of the enzyme dihydrofolate reductase , which catalyzes the reduction of dihydrofolate to tetrahydrofolate. The similarity between the structures of dihydrofolate and this drug are shown in the accompanying figure. This type of inhibition can be overcome with high substrate concentration. In some cases,
8288-422: The enzyme converts the substrates into different molecules known as products . Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost
8400-403: The enzyme. As a result, the substrate does not simply bind to a rigid active site; the amino acid side-chains that make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as glycosidases , the substrate molecule also changes shape slightly as it enters the active site. The active site continues to change until
8512-427: The enzyme. For example, the enzyme can be soluble and upon activation bind to a lipid in the plasma membrane and then act upon molecules in the plasma membrane. Allosteric sites are pockets on the enzyme, distinct from the active site, that bind to molecules in the cellular environment. These molecules then cause a change in the conformation or dynamics of the enzyme that is transduced to the active site and thus affects
8624-510: The expression, and so findings may or may not be entirely identical to native expression: For example, iron has been found by Bakouh et al 2017 to be an important substrate for one such transporter in X. l. oocytes, but as of 2020 iron is merely presumptively involved in native expression of the same gene. Xenbase is the Model Organism Database (MOD) for both Xenopus laevis and Xenopus tropicalis . Xenbase hosts
8736-580: The family Pipidae . Its name is derived from the short black claws on its feet. The word Xenopus means 'strange foot' and laevis means 'smooth'. The species is found throughout much of Sub-Saharan Africa ( Nigeria and Sudan to South Africa ), and in isolated, introduced populations in North America, South America, Europe, and Asia. All species of the family Pipidae are tongueless, toothless and completely aquatic. They use their hands to shove food in their mouths and down their throats and
8848-548: The female's body (see frog reproduction ). Of the seven amplexus modes (positions in which frogs mate), these frogs are found breeding in inguinal amplexus, where the male clasps the female in front of the female's back legs until eggs are laid, and the male fertilizes the egg mass with the release of sperm. African clawed frogs are highly adaptable and will lay their eggs whenever conditions allow it. During wet rainy seasons they will travel to other ponds or puddles of water to search for food and new ponds. During times of drought,
8960-550: The full details and release information regarding the current v10 Xenopus laevis genome released in 2022. The clawed frog have been kept as pets and research subjects since as early as the 1950s. They are extremely hardy and long lived, having been known to live up to 20 or even 30 years in captivity. African clawed frogs are frequently mislabeled as African dwarf frogs in pet stores. Identifiable differences are: African clawed frogs are voracious predators and easily adapt to many habitats. For this reason, they can easily become
9072-413: The inhibitor can bind to a site other than the binding-site of the usual substrate and exert an allosteric effect to change the shape of the usual binding-site. Xenopus laevis X. boiei Wagler 1827 The African clawed frog ( Xenopus laevis ), also known as simply xenopus , African clawed toad , African claw-toed frog or the platanna ) is a species of African aquatic frog of
9184-468: The irregular regulation is responsible for the disrupted A to I editing pattern seen in HCC and that ADAR1 acts as an oncogene in this context whilst ADAR2 has tumor suppressor activities. The imbalance in ADAR expression could change the frequency of A to I transitions in the protein coding region of genes, resulting in mutated proteins which drive the disease. The dysregulation of ADAR1 and ADAR2 could be used as
9296-615: The larval gills, tail and fins in amphibians metamorphosis , and stimulate the evolution of their nervous system transforming the aquatic, vegetarian tadpole into the terrestrial, carnivorous frog. Stem cells of this frog were used to create xenobots . Early work on sequencing of the X. laevis genome was started when the Wallingford and Marcotte labs obtained funding from the Texas Institute for Drug and Diagnostic Development (TI3D), in conjunction with projects funded by
9408-454: The majority of modern phyla , indicates that RNA editing is essential in regulating genes for metazoan organisms. ADAR has not been discovered in a variety of non-metazoan eukaryotes, such as plants , fungi and choanoflagellates . ADARs are suggested to have two functions: to increase diversity of the proteome by inducing creation of harmless non-genomically encoded proteins, and protecting crucial translational sites. The conventional belief
9520-444: The male. This frog has smooth slippery skin which is multicolored on its back with blotches of olive gray or brown. The underside is creamy white with a yellow tinge. Male and female frogs can be easily distinguished through the following differences. Male frogs are small and slim, while females are larger and more rotund. Males have black patches on their hands and arms which aid in grabbing onto females during amplexus. Females have
9632-474: The mixture. He named the enzyme that brought about the fermentation of sucrose " zymase ". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are usually named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate (e.g., lactase is the enzyme that cleaves lactose ) or to
9744-671: The most well-grounded marker of amyotrophic lateral sclerosis (ALS) is the TAR DNA-binding protein (TDP-43) . When there is failure of RNA-editing due to downregulation of TDP-43, motor neurons devoid of ADAR2 enzymes express unregulated, leading to abnormally permeable Ca channels. ADAR2 knockout mice show signs of ALS phenotype similarity. Current researchers are developing a molecular targeting therapy by normalizing expression of ADAR2. (ADAR)-induced A-to-I RNA editing may elicit dangerous amino acid mutations. Editing mRNA typically imparts missense mutations leading to alterations in
9856-440: The mutants were not able to bind to dsRNA but were still able to dimerize , suggesting they may bind based on protein-protein interactions. ADAR1 is one of multiple genes which often contribute to Aicardi–Goutières syndrome when mutated. Aicardi–Goutières syndrome is a genetic inflammatory disease primarily affecting the skin and the brain and it is characterized by high levels of IFN-α in cerebral spinal fluid. The inflammation
9968-609: The nervous system. In vitro studies have also shown that ADAR3 might play a role in the regulation of ADAR one and two. ADARs catalyze the hydrolytic deamination reaction from adenosine to inosine. An activated water molecule will react with adenosine in a nucleophilic substitution reaction with the carbon-6 amine group. A hydrated intermediate will exist for a short period of time, then the amine group will leave as an ammonia ion. [REDACTED] In humans, ADAR enzymes have two to three amino-terminal dsRNA binding domains (dsRBDs), and one carboxy terminal catalytic deaminase domain. In
10080-403: The nucleus, while ADAR1p150 shuffles between the nucleus and the cytoplasm, mostly present in the cytoplasm. ADAR3 (ADARB2) ADAR 3 varies from the other two forms of ADAR in that it is only found within brain tissue. It also is considered to be inactive when it comes to catalytic activity. ADAR3 has been found to be linked to memory and learning in mice, showing that it plays a crucial role in
10192-444: The oocyte or developing embryo, scientists can study the protein products in a controlled system. This allows rapid functional expression of manipulated DNAs (or mRNA ). This is particularly useful in electrophysiology , where the ease of recording from the oocyte makes expression of membrane channels attractive. One challenge of oocyte work is eliminating native proteins that might confound results, such as membrane channels native to
10304-528: The precise orientation and dynamics of the active site. In some enzymes, no amino acids are directly involved in catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors . Enzyme structures may also contain allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity. A small number of RNA -based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these
10416-406: The reaction and releases the product. This work was further developed by G. E. Briggs and J. B. S. Haldane , who derived kinetic equations that are still widely used today. Enzyme rates depend on solution conditions and substrate concentration . To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation
10528-733: The reaction rate of the enzyme. In this way, allosteric interactions can either inhibit or activate enzymes. Allosteric interactions with metabolites upstream or downstream in an enzyme's metabolic pathway cause feedback regulation, altering the activity of the enzyme according to the flux through the rest of the pathway. Some enzymes do not need additional components to show full activity. Others require non-protein molecules called cofactors to be bound for activity. Cofactors can be either inorganic (e.g., metal ions and iron–sulfur clusters ) or organic compounds (e.g., flavin and heme ). These cofactors serve many purposes; for instance, metal ions can help in stabilizing nucleophilic species within
10640-410: The same enzymatic activity have been called non-homologous isofunctional enzymes . Horizontal gene transfer may spread these genes to unrelated species, especially bacteria where they can replace endogenous genes of the same function, leading to hon-homologous gene displacement. Enzymes are generally globular proteins , acting alone or in larger complexes . The sequence of the amino acids specifies
10752-751: The stomach contents of feral clawed frogs in California have revealed large amounts of the frog's larvae. Clawed frog larvae are filter feeders and collect nutrients from plankton, allowing adult frogs that consume the tadpoles to have access to these nutrients. This allows clawed frogs to survive in areas that have little to no other food sources. Clawed frogs are nocturnal and most reproductive activity and feeding occurs after dark. Male clawed frogs are very promiscuous and will grab onto other males and even other species of frogs. Male frogs that are grasped will make release calls and attempt to break free. If not feeding, clawed frogs will just sit motionless on top of
10864-412: The structure which in turn determines the catalytic activity of the enzyme. Although structure determines function, a novel enzymatic activity cannot yet be predicted from structure alone. Enzyme structures unfold ( denature ) when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity. Enzyme denaturation is normally linked to temperatures above
10976-519: The substrate is completely bound, at which point the final shape and charge distribution is determined. Induced fit may enhance the fidelity of molecular recognition in the presence of competition and noise via the conformational proofreading mechanism. Enzymes can accelerate reactions in several ways, all of which lower the activation energy (ΔG , Gibbs free energy ) Enzymes may use several of these mechanisms simultaneously. For example, proteases such as trypsin perform covalent catalysis using
11088-590: The substrate or floating, legs splayed below, at the waters surface with their nostrils and eyes sticking out. The clawed frog liver responds to low temperatures by increasing production of type II iodothyronine deiodinase through increased food intake . This in turn spurs the thyroid to increase T 3 to increase body temperature . (This T 3 increase also induces germ cell apoptosis , mediated through genes left over from tadpole metamorphosis.) The effects of provocation of T hormone release are broadly differentiated by where it starts: If centrally, within
11200-405: The substrates. Enzymes can therefore distinguish between very similar substrate molecules to be chemoselective , regioselective and stereospecific . Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome . Some of these enzymes have " proof-reading " mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in
11312-561: The super short generation time , or genetic simplicity generally desired in genetic model organisms , it is an important model organism in developmental biology , cell biology , toxicology and neurobiology . X. laevis takes 1 to 2 years to reach sexual maturity and, like most of its genus, it is tetraploid . It does have a large and easily manipulated embryo , however. The ease of manipulation in amphibian embryos has given them an important place in historical and modern developmental biology. A related species, Xenopus tropicalis ,
11424-399: The synthesis of antibiotics . Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew. By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and
11536-438: The type of reaction (e.g., DNA polymerase forms DNA polymers). The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others (such as Nobel laureate Richard Willstätter ) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner showed that
11648-676: The water except to migrate to new water bodies during droughts or other disturbances. Clawed frogs have powerful legs that help them move quickly both underwater and on land. Feral clawed frogs in South Wales have been found to travel up to 2 kilometres (1.2 mi) between locations. The feet of Xenopus species have three black claws on the last three digits. These claws are used to rip apart food and scratch predators. Clawed frogs are carnivores and will eat both living and dead prey including fish, tadpoles, crustaceans, annelids, arthropods, and more. Clawed frogs will try to consume anything that
11760-654: The wide breadth of Xenopus research stems from the additional fact that cell-free extracts made from Xenopus are a premier in vitro system for studies of fundamental aspects of cell and molecular biology. Thus, Xenopus is the only vertebrate model system that allows for high-throughput in vivo analyses of gene function and high-throughput biochemistry. Xenopus oocytes are a leading system in their own right for studies of various systems, including ion transport and channel physiology. Xanthos et al 2001 uses oocytes to uncover T-box expression earlier than previously found in vertebrates. Although X. laevis does not have
11872-555: The wild - Found at higher densities in artificial water bodies such as ponds, dams and irrigation canals, rather than in natural lagoons or streams or rivers. - There is no evidence of predation on native anurans, but rather on their own larvae. - They face predation from native birds. Cause of concerns from African clawed frogs - They are reaching both lower and higher altitudes than formerly estimated. - They are able to migrate overland to colonise other water bodies, causing ecological disruption and spreading diseases. X. laevis in
11984-472: The wild are commonly infected by various parasites , including monogeneans in the urinary bladder . Xenopus embryos and eggs are a popular model system for a wide variety of biological studies, in part because they have the potential to lay eggs throughout the year. This animal is widely used because of its powerful combination of experimental tractability and close evolutionary relationship with humans, at least compared to many model organisms. For
12096-614: The wild, X. laevis are native to wetlands , ponds, and lakes across arid/semiarid regions of Sub-Saharan Africa . X. laevis and X. muelleri occur along the western boundary of the Great African Rift . The people of the sub-Saharan are generally very familiar with this frog, and some cultures use it as a source of protein, an aphrodisiac , or as fertility medicine . Two historic outbreaks of priapism have been linked to consumption of frog legs from frogs that ate insects containing cantharidin . African clawed frogs in
12208-486: The yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." In 1877, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme , which comes from Ancient Greek ἔνζυμον (énzymon) ' leavened , in yeast', to describe this process. The word enzyme
12320-581: Was first done for lysozyme , an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail. Enzymes can be classified by two main criteria: either amino acid sequence similarity (and thus evolutionary relationship) or enzymatic activity. Enzyme activity . An enzyme's name
12432-528: Was used as a simple and reliable test up through to the 1960s. In the late 1940s, Carlos Galli Mainini found in separate studies that male specimens of Xenopus and Bufo could be used to indicate pregnancy Today, commercially available hCG is injected into Xenopus males and females to induce mating behavior and to breed these frogs in captivity at any time of the year. Xenopus has long been an important tool for in vivo studies in molecular, cell, and developmental biology of vertebrate animals. However,
12544-399: Was used later to refer to nonliving substances such as pepsin , and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin , he found that sugar was fermented by yeast extracts even when there were no living yeast cells in
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