Misplaced Pages

#557442

83-431: NAT enzymes are differentiated by the presence of a conserved catalytic triad that favors aromatic amine and hydrazine substrates. NATs catalyze the acetylation of small molecules through a double displacement reaction called the ping pong bi bi reaction. The mechanism consists of two sequential reactions. In reaction one acetyl-CoA initially binds to the enzyme and acetylates Cys. In reaction two, after acetyl-CoA

166-465: A Cys-His-Asn triad). The enzymology of proteases provides some of the clearest known examples of convergent evolution at a molecular level. The same geometric arrangement of triad residues occurs in over 20 separate enzyme superfamilies . Each of these superfamilies is the result of convergent evolution for the same triad arrangement within a different structural fold . This is because there are limited productive ways to arrange three triad residues,

249-409: A base in the triad at very low pH. The triad is hypothesised to be an adaptation to specific environments like acidic hot springs (e.g. kumamolysin ) or cell lysosome (e.g. tripeptidyl peptidase ). The endothelial protease vasohibin uses a cysteine as the nucleophile, but a serine to coordinate the histidine base. Despite the serine being a poor acid, it is still effective in orienting

332-402: A base. This unusual triad occurs only in one superfamily of amidases. In this case, the lysine acts to polarise the middle serine. The middle serine then forms two strong hydrogen bonds to the nucleophilic serine to activate it (one with the side chain hydroxyl and the other with the backbone amide). The middle serine is held in an unusual cis orientation to facilitate precise contacts with

415-484: A bird feeds a brood parasite such as a cuckoo , it is unwittingly extending its phenotype; and when genes in an orchid affect orchid bee behavior to increase pollination, or when genes in a peacock affect the copulatory decisions of peahens, again, the phenotype is being extended. Genes are, in Dawkins's view, selected by their phenotypic effects. Other biologists broadly agree that the extended phenotype concept

498-425: A bulkier van der Waals radius and if mutated to serine can be trapped in unproductive orientations in the active site. Very rarely, the selenium atom of the uncommon amino acid selenocysteine is used as a nucleophile. The deprotonated Se state is strongly favoured when in a catalytic triad. Since no natural amino acids are strongly nucleophilic, the base in a catalytic triad polarises and deprotonates

581-399: A covalent intermediate with the substrate that is then resolved to complete catalysis. Catalytic triads perform covalent catalysis using a residue as a nucleophile. The reactivity of the nucleophilic residue is increased by the functional groups of the other triad members. The nucleophile is polarised and oriented by the base, which is itself bound and stabilised by the acid. Catalysis

664-515: A few notable differences. Due to cysteine's low p K a , the importance of the Asp to catalysis varies and several cysteine proteases are effectively Cys-His dyads (e.g. hepatitis A virus protease), whilst in others the cysteine is already deprotonated before catalysis begins (e.g. papain). This triad is also used by some amidases, such as N -glycanase to hydrolyse non-peptide C-N bonds. The triad of cytomegalovirus protease uses histidine as both

747-518: A gene has on its surroundings, including other organisms, as an extended phenotype, arguing that "An animal's behavior tends to maximize the survival of the genes 'for' that behavior, whether or not those genes happen to be in the body of the particular animal performing it." For instance, an organism such as a beaver modifies its environment by building a beaver dam ; this can be considered an expression of its genes , just as its incisor teeth are—which it uses to modify its environment. Similarly, when

830-529: A large part of the Human Genome Project . Phenomics has applications in agriculture. For instance, genomic variations such as drought and heat resistance can be identified through phenomics to create more durable GMOs. Phenomics may be a stepping stone towards personalized medicine , particularly drug therapy . Once the phenomic database has acquired enough data, a person's phenomic information can be used to select specific drugs tailored to

913-401: A lower p K a (by 5 units). Serine is therefore more dependent than cysteine on optimal orientation of the acid-base triad members to reduce its p K a in order to achieve concerted deprotonation with catalysis. The low p K a of cysteine works to its disadvantage in the resolution of the first tetrahedral intermediate as unproductive reversal of the original nucleophilic attack is

SECTION 10

#1732794493558

996-537: A multidimensional search space with several neurobiological levels, spanning the proteome, cellular systems (e.g., signaling pathways), neural systems and cognitive and behavioural phenotypes." Plant biologists have started to explore the phenome in the study of plant physiology. In 2009, a research team demonstrated the feasibility of identifying genotype–phenotype associations using electronic health records (EHRs) linked to DNA biobanks . They called this method phenome-wide association study (PheWAS). Inspired by

1079-453: A particular enzyme is expressed at high levels, the organism may produce more of that enzyme and exhibit a particular trait as a result. On the other hand, if the gene is expressed at low levels, the organism may produce less of the enzyme and exhibit a different trait. Gene expression is regulated at various levels and thus each level can affect certain phenotypes, including transcriptional and post-transcriptional regulation. Changes in

1162-680: A proton as the remaining OH attacks the acyl-enzyme intermediate. The same triad has also convergently evolved in α/β hydrolases such as some lipases and esterases , however orientation of the triad members is reversed. Additionally, brain acetyl hydrolase (which has the same fold as a small G-protein ) has also been found to have this triad. The second most studied triad is the Cysteine-Histidine-Aspartate motif. Several families of cysteine proteases use this triad set, for example TEV protease and papain . The triad acts similarly to serine protease triads, with

1245-492: A range of other proteins. Similarly, catalytic triad mimics have been created in small organic molecules like diaryl diselenide, and displayed on larger polymers like Merrifield resins , and self-assembling short peptide nanostructures. The sophistication of the active site network causes residues involved in catalysis (and residues in contact with these) to be highly evolutionarily conserved . However, there are examples of divergent evolution in catalytic triads, both in

1328-436: A second substrate. If this substrate is water then the result is hydrolysis; if it is an organic molecule then the result is transfer of that molecule onto the first substrate. Attack by this second substrate forms a new tetrahedral intermediate, which resolves by ejecting the enzyme's nucleophile, releasing the second product and regenerating free enzyme. The side-chain of the nucleophilic residue performs covalent catalysis on

1411-408: A substrate ( hydrolases ) or to transfer one portion of a substrate over to a second substrate ( transferases ). Triads are an inter-dependent set of residues in the active site of an enzyme and act in concert with other residues (e.g. binding site and oxyanion hole ) to achieve nucleophilic catalysis . These triad residues act together to make the nucleophile member highly reactive , generating

1494-684: A superfamily (with the same fold ) contains families that use different nucleophiles. Such nucleophile switches have occurred several times during evolutionary history, however the mechanisms by which this happen are still unclear. Within protease superfamilies that contain a mixture of nucleophiles (e.g. the PA clan ), families are designated by their catalytic nucleophile (C=cysteine proteases, S=serine proteases). A further subclass of catalytic triad variants are pseudoenzymes , which have triad mutations that make them catalytically inactive, but able to function as binding or structural proteins. For example,

1577-574: Is caused by an irreversible formation of a Cisplatin adduct with the active-site cysteine residue. The C-terminus helps bind acetyl CoA and differs among NATs including prokaryotic homologues. NAT1 and NAT2 have different but overlapping substrate specificities. Human NAT1 preferentially acetylates 4-aminobenzoic acid (PABA), 4 amino salicylic acid , sulfamethoxazole , and sulfanilamide . Human NAT2 preferentially acetylates isoniazid (treatment for tuberculosis ), hydralazine , procainamide , dapsone , aminoglutethimide , and sulfamethazine . NAT2

1660-463: Is found growing in two different habitats in Sweden. One habitat is rocky, sea-side cliffs , where the plants are bushy with broad leaves and expanded inflorescences ; the other is among sand dunes where the plants grow prostrate with narrow leaves and compact inflorescences. These habitats alternate along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in, determine

1743-553: Is involved in the metabolism of xenobiotics , which can lead to both the inactivation of drugs and formation of toxic metabolites that can be carcinogenic . The biotransformation of xenobiotics may occur in three phases. In phase I, reactive and polar groups are introduced into the substrates. In phase II, conjugation of xenobiotics with charged species occurs, and in phase III additional modifications are made, with efflux mechanisms leading to excretion by transporters. A genome-wide association study (GWAS) identified human NAT2 as

SECTION 20

#1732794493558

1826-419: Is performed in two stages. First, the activated nucleophile attacks the carbonyl carbon and forces the carbonyl oxygen to accept an electron pair, leading to a tetrahedral intermediate . The build-up of negative charge on this intermediate is typically stabilized by an oxyanion hole within the active site. The intermediate then collapses back to a carbonyl, ejecting the first half of the substrate, but leaving

1909-417: Is problematic. A proposed definition for both terms as the "physical totality of all traits of an organism or of one of its subsystems" was put forth by Mahner and Kary in 1997, who argue that although scientists tend to intuitively use these and related terms in a manner that does not impede research, the terms are not well defined and usage of the terms is not consistent. Some usages of the term suggest that

1992-633: Is released, the acetyl acceptor interacts with the acetylated enzyme to form product. This second reaction is independent of the acetyl donor since it leaves the enzyme before the acetyl acceptor binds. However, like with many ping pong bi bi reactions, its possible there is competition between the acetyl donor and acetyl acceptor for the unacetylated enzyme. This leads to substrate-dependent inhibition at high concentrations. The two NAT enzymes in humans are NAT1 and NAT2 . Mice and rats express three enzymes, NAT1, NAT2, and NAT3. NAT1 and NAT2 have been found to be closely related in species examined thus far, since

2075-478: Is relevant, but consider that its role is largely explanatory, rather than assisting in the design of experimental tests. Phenotypes are determined by an interaction of genes and the environment, but the mechanism for each gene and phenotype is different. For instance, an albino phenotype may be caused by a mutation in the gene encoding tyrosinase which is a key enzyme in melanin formation. However, exposure to UV radiation can increase melanin production, hence

2158-426: Is resolved by water, the result is hydrolysis of the substrate. However, if the intermediate is resolved by attack by a second substrate, then the enzyme acts as a transferase . For example, attack by an acyl group results in an acyltransferase reaction. Several families of transferase enzymes have evolved from hydrolases by adaptation to exclude water and favour attack of a second substrate. In different members of

2241-717: Is similar to cysteine, but contains a selenium atom instead of a sulfur. A selenocysteine residue is found in the active site of thioredoxin reductase , which uses the selenol group for reduction of disulfide in thioredoxin. In addition to naturally occurring types of catalytic triads, protein engineering has been used to create enzyme variants with non-native amino acids, or entirely synthetic amino acids. Catalytic triads have also been inserted into otherwise non-catalytic proteins, or protein mimics. Subtilisin (a serine protease) has had its oxygen nucleophile replaced with each of sulfur, selenium , or tellurium . Cysteine and selenocysteine were inserted by mutagenesis , whereas

2324-402: Is so high (p K a =11), a glutamate and several other residues act as the acid to stabilise its deprotonated state during the catalytic cycle. Threonine proteases use their N -terminal amide as the base, since steric crowding by the catalytic threonine's methyl prevents other residues from being close enough. The acidic triad member forms a hydrogen bond with the basic residue. This aligns

2407-412: Is the hypothesized pre-cellular stage in the evolutionary history of life on earth, in which self-replicating RNA molecules proliferated prior to the evolution of DNA and proteins. The folded three-dimensional physical structure of the first RNA molecule that possessed ribozyme activity promoting replication while avoiding destruction would have been the first phenotype, and the nucleotide sequence of

2490-479: Is the set of observable characteristics or traits of an organism . The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological properties, its behavior , and the products of behavior. An organism's phenotype results from two basic factors: the expression of an organism's genetic code (its genotype ) and the influence of environmental factors. Both factors may interact, further affecting

2573-647: The N -terminal residue as a nucleophile: Superfamily PB (proteasomes using the Ntn fold) and Superfamily PE ( acetyltransferases using the DOM fold) This commonality of active site structure in completely different protein folds indicates that the active site evolved convergently in those superfamilies. Families of threonine proteases Phenotype In genetics , the phenotype (from Ancient Greek φαίνω ( phaínō )  'to appear, show' and τύπος ( túpos )  'mark, type')

N-acetyltransferase - Misplaced Pages Continue

2656-425: The active site of some enzymes . Catalytic triads are most commonly found in hydrolase and transferase enzymes (e.g. proteases , amidases , esterases , acylases , lipases and β-lactamases ). An acid - base - nucleophile triad is a common motif for generating a nucleophilic residue for covalent catalysis . The residues form a charge-relay network to polarise and activate the nucleophile, which attacks

2739-550: The genotype–phenotype distinction in 1911 to make clear the difference between an organism's hereditary material and what that hereditary material produces. The distinction resembles that proposed by August Weismann (1834–1914), who distinguished between germ plasm (heredity) and somatic cells (the body). More recently, in The Selfish Gene (1976), Dawkins distinguished these concepts as replicators and vehicles. Despite its seemingly straightforward definition,

2822-799: The heparin -binding protein Azurocidin is a member of the PA clan, but with a glycine in place of the nucleophile and a serine in place of the histidine. Similarly, RHBDF1 is a homolog of the S54 family rhomboid proteases with an alanine in the place of the nucleophilic serine. In some cases, pseudoenzymes may still have an intact catalytic triad but mutations in the rest of the protein remove catalytic activity. The CA clan contains catalytically inactive members with mutated triads ( calpamodulin has lysine in place of its cysteine nucleophile) and with intact triads but inactivating mutations elsewhere (rat testin retains

2905-593: The hydroxyl (OH) of serine and the thiol /thiolate ion (SH/S ) of cysteine. Alternatively, threonine proteases use the secondary hydroxyl of threonine, however due to steric hindrance of the side chain's extra methyl group such proteases use their N -terminal amide as the base, rather than a separate amino acid. Use of oxygen or sulfur as the nucleophilic atom causes minor differences in catalysis. Compared to oxygen , sulfur 's extra d orbital makes it larger (by 0.4 Å) and softer, allows it to form longer bonds (d C-X and d X-H by 1.3-fold), and gives it

2988-480: The substrate , forming a covalent intermediate which is then hydrolysed to release the product and regenerate free enzyme. The nucleophile is most commonly a serine or cysteine amino acid, but occasionally threonine or even selenocysteine . The 3D structure of the enzyme brings together the triad residues in a precise orientation, even though they may be far apart in the sequence ( primary structure ). As well as divergent evolution of function (and even

3071-409: The substrate . The lone pair of electrons present on the oxygen or sulfur attacks the electropositive carbonyl carbon. The 20 naturally occurring biological amino acids do not contain any sufficiently nucleophilic functional groups for many difficult catalytic reactions . Embedding the nucleophile in a triad increases its reactivity for efficient catalysis. The most commonly used nucleophiles are

3154-499: The 1990s and 2000s began classing proteases into structurally related enzyme superfamilies and so acts as a database of the convergent evolution of triads in over 20 superfamilies. Understanding how chemical constraints on evolution led to the convergence of so many enzyme families on the same triad geometries has developed in the 2010s. Since their initial discovery, there have been increasingly detailed investigations of their exact catalytic mechanism. Of particular contention in

3237-439: The 1990s and 2000s was whether low-barrier hydrogen bonding contributed to catalysis, or whether ordinary hydrogen bonding is sufficient to explain the mechanism. The massive body of work on the charge-relay, covalent catalysis used by catalytic triads has led to the mechanism being the best characterised in all of biochemistry. Enzymes that contain a catalytic triad use it for one of two reaction types: either to split

3320-492: The acetylator phenotype is described as either slow, intermediate, or rapid. Beyond modifying enzymatic activity, epidemiological studies have found an association of NAT2 polymorphisms with various cancers, likely from varying environmental carcinogens . Indeed, NAT2 is highly polymorphic in several human populations. Polymorphisms of NAT2 include the single amino acid substitutions R64Q, I114T, D122N, L137F, Q145P, R197Q, and G286E. These are classified as slow acetylators, while

3403-422: The acid and base triad members. Removing the acid histidine results in only a 10-fold activity loss (compared to >10,000-fold when aspartate is removed from chymotrypsin). This triad has been interpreted as a possible way of generating a less active enzyme to control cleavage rate. An unusual triad is found in sedolisin proteases. The low p K a of the glutamate carboxylate group means that it only acts as

N-acetyltransferase - Misplaced Pages Continue

3486-421: The base member of the triad is the N -terminal amide which polarises an ordered water which, in turn, deprotonates the catalytic hydroxyl to increase its reactivity. Similarly, there exist equivalent 'serine only' and 'cysteine only' configurations such as penicillin acylase G and penicillin acylase V which are evolutionarily related to the proteasome proteases. Again, these use their N -terminal amide as

3569-412: The basic residue by restricting its side-chain rotation, and polarises it by stabilising its positive charge. Two amino acids have acidic side chains at physiological pH (aspartate or glutamate) and so are the most commonly used for this triad member. Cytomegalovirus protease uses a pair of histidines, one as the base, as usual, and one as the acid. The second histidine is not as effective an acid as

3652-450: The concept of the phenotype has hidden subtleties. It may seem that anything dependent on the genotype is a phenotype, including molecules such as RNA and proteins . Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable (for example by Western blotting ) and are thus part of the phenotype; human blood groups are an example. It may seem that this goes beyond

3735-517: The context of phenotype prediction. Although a phenotype is the ensemble of observable characteristics displayed by an organism, the word phenome is sometimes used to refer to a collection of traits, while the simultaneous study of such a collection is referred to as phenomics . Phenomics is an important field of study because it can be used to figure out which genomic variants affect phenotypes which then can be used to explain things like health, disease, and evolutionary fitness. Phenomics forms

3818-483: The corresponding amino acid sequence of a gene may change the frequency of guanine - cytosine base pairs ( GC content ). These base pairs have a higher thermal stability ( melting point ) than adenine - thymine , a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content. Richard Dawkins described a phenotype that included all effects that

3901-415: The environment plays a role in this phenotype as well. For most complex phenotypes the precise genetic mechanism remains unknown. For instance, it is largely unclear how genes determine the shape of bones or the human ear. Gene expression plays a crucial role in determining the phenotypes of organisms. The level of gene expression can affect the phenotype of an organism. For example, if a gene that codes for

3984-496: The enzyme backbone and the substrate. These examples reflect the intrinsic chemical and physical constraints on enzymes, leading evolution to repeatedly and independently converge on equivalent solutions. The same triad geometries been converged upon by serine proteases such as the chymotrypsin and subtilisin superfamilies. Similar convergent evolution has occurred with cysteine proteases such as viral C3 protease and papain superfamilies. These triads have converged to almost

4067-426: The enzyme into an oxidoreductase . When the nucleophile of TEV protease was converted from cysteine to serine, it protease activity was strongly reduced, but was able to be restored by directed evolution . Non-catalytic proteins have been used as scaffolds, having catalytic triads inserted into them which were then improved by directed evolution. The Ser-His-Asp triad has been inserted into an antibody, as well as

4150-439: The evolution from genotype to genome to pan-genome , a concept of exploring the relationship ultimately among pan-phenome, pan-genome , and pan- envirome was proposed in 2023. Phenotypic variation (due to underlying heritable genetic variation ) is a fundamental prerequisite for evolution by natural selection . It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects

4233-449: The evolutionarily unrelated papain and subtilisin proteases were found to contain analogous triads. The 'charge-relay' mechanism for the activation of the nucleophile by the other triad members was proposed in the late 1960s. As more protease structures were solved by X-ray crystallography in the 1970s and 80s, homologous (such as TEV protease ) and analogous (such as papain) triads were found. The MEROPS classification system in

SECTION 50

#1732794493558

4316-440: The false statement that a "mutation has no phenotype". Behaviors and their consequences are also phenotypes, since behaviors are observable characteristics. Behavioral phenotypes include cognitive, personality, and behavioral patterns. Some behavioral phenotypes may characterize psychiatric disorders or syndromes. A phenome is the set of all traits expressed by a cell , tissue , organ , organism , or species . The term

4399-450: The first active site, a cysteine triad hydrolyses a glutamine substrate to release free ammonia. The ammonia then diffuses though an internal tunnel in the enzyme to the second active site, where it is transferred to a second substrate. Divergent evolution of active site residues is slow, due to strong chemical constraints. Nevertheless, some protease superfamilies have evolved from one nucleophile to another. This can be inferred when

4482-541: The genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection. The interaction between genotype and phenotype has often been conceptualized by the following relationship: A more nuanced version of the relationship is: Genotypes often have much flexibility in the modification and expression of phenotypes; in many organisms these phenotypes are very different under varying environmental conditions. The plant Hieracium umbellatum

4565-415: The histidine in the catalytic triad. Some homologues alternatively have a threonine instead of serine at the acid location. Threonine proteases, such as the proteasome protease subunit and ornithine acyltransferases use the secondary hydroxyl of threonine in a manner analogous to the use of the serine primary hydroxyl . However, due to the steric interference of the extra methyl group of threonine,

4648-721: The individual. Large-scale genetic screens can identify the genes or mutations that affect the phenotype of an organism. Analyzing the phenotypes of mutant genes can also aid in determining gene function. Most genetic screens have used microorganisms, in which genes can be easily deleted. For instance, nearly all genes have been deleted in E. coli and many other bacteria , but also in several eukaryotic model organisms such as baker's yeast and fission yeast . Among other discoveries, such studies have revealed lists of essential genes . More recently, large-scale phenotypic screens have also been used in animals, e.g. to study lesser understood phenotypes such as behavior . In one screen,

4731-408: The last 6,500 years in western and central Eurasian people, suggesting slow acetylation gave an evolutionary advantage to this population, despite the recent unfavorable epidemiological health outcomes data. The following is a list of human genes that encode N-acetyltransferase enzymes: Catalytic triad A catalytic triad is a set of three coordinated amino acids that can be found in

4814-626: The levels of gene expression can be influenced by a variety of factors, such as environmental conditions, genetic variations, and epigenetic modifications. These modifications can be influenced by environmental factors such as diet, stress, and exposure to toxins, and can have a significant impact on an individual's phenotype. Some phenotypes may be the result of changes in gene expression due to these factors, rather than changes in genotype. An experiment involving machine learning methods utilizing gene expressions measured from RNA sequencing found that they can contain enough signal to separate individuals in

4897-421: The methyl clashes with either the enzyme backbone or histidine base. When the nucleophile of a serine protease was mutated to threonine, the methyl occupied a mixture of positions, most of which prevented substrate binding. Consequently, the catalytic residue of a threonine protease is located at its N -terminus. Two evolutionarily independent enzyme superfamilies with different protein folds are known to use

4980-409: The more common aspartate or glutamate, leading to a lower catalytic efficiency. The Serine-Histidine-Aspartate motif is one of the most thoroughly characterised catalytic motifs in biochemistry. The triad is exemplified by chymotrypsin , a model serine protease from the PA superfamily which uses its triad to hydrolyse protein backbones. The aspartate is hydrogen bonded to the histidine, increasing

5063-448: The more favourable breakdown product. The triad base is therefore preferentially oriented to protonate the leaving group amide to ensure that it is ejected to leave the enzyme sulfur covalently bound to the substrate N-terminus. Finally, resolution of the acyl-enzyme (to release the substrate C-terminus) requires serine to be re-protonated whereas cysteine can leave as S . Sterically , the sulfur of cysteine also forms longer bonds and has

SECTION 60

#1732794493558

5146-478: The non-natural amino acid, tellurocysteine , was inserted using auxotrophic cells fed with synthetic tellurocysteine. These elements are all in the 16th periodic table column ( chalcogens ), so have similar properties. In each case, changing the nucleophile lowered the enzyme's protease activity, but increased a new activity. A sulfur nucleophile improved the enzymes transferase activity (sometimes called subtiligase). Selenium and tellurium nucleophiles converted

5229-400: The nucleophile to increase its reactivity. Additionally, it protonates the first product to aid leaving group departure. The base is most commonly histidine since its p K a allows for effective base catalysis, hydrogen bonding to the acid residue, and deprotonation of the nucleophile residue. β-lactamases such as TEM-1 use a lysine residue as the base. Because lysine's p K a

5312-619: The number of putative mutants (see table for details). Putative mutants are then tested for heritability in order to help determine the inheritance pattern as well as map out the mutations. Once they have been mapped out, cloned, and identified, it can be determined whether a mutation represents a new gene or not. These experiments showed that mutations in the rhodopsin gene affected vision and can even cause retinal degeneration in mice. The same amino acid change causes human familial blindness , showing how phenotyping in animals can inform medical diagnostics and possibly therapy. The RNA world

5395-411: The original intentions of the concept with its focus on the (living) organism in itself. Either way, the term phenotype includes inherent traits or characteristics that are observable or traits that can be made visible by some technical procedure. The term "phenotype" has sometimes been incorrectly used as a shorthand for the phenotypic difference between a mutant and its wild type , which would lead to

5478-408: The other two triad residues. The triad is further unusual in that the lysine and cis -serine both act as the base in activating the catalytic serine, but the same lysine also performs the role of the acid member as well as making key structural contacts. The rare, but naturally occurring amino acid selenocysteine (Sec), can also be found as the nucleophile in some catalytic triads. Selenocysteine

5561-415: The p K a of its imidazole nitrogen from 7 to around 12. This allows the histidine to act as a powerful general base and to activate the serine nucleophile. It also has an oxyanion hole consisting of several backbone amides which stabilises charge build-up on intermediates. The histidine base aids the first leaving group by donating a proton, and also activates the hydrolytic water substrate by abstracting

5644-438: The phenome of a given organism is best understood as a kind of matrix of data representing physical manifestation of phenotype. For example, discussions led by A. Varki among those who had used the term up to 2003 suggested the following definition: "The body of information describing an organism's phenotypes, under the influences of genetic and environmental factors". Another team of researchers characterize "the human phenome [as]

5727-531: The phenotype that grows. An example of random variation in Drosophila flies is the number of ommatidia , which may vary (randomly) between left and right eyes in a single individual as much as they do between different genotypes overall, or between clones raised in different environments. The concept of phenotype can be extended to variations below the level of the gene that affect an organism's fitness. For example, silent mutations that do not change

5810-590: The phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic . A well-documented example of polymorphism is Labrador Retriever coloring ; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. Richard Dawkins in 1978 and then again in his 1982 book The Extended Phenotype suggested that one can regard bird nests and other built structures such as caddisfly larva cases and beaver dams as "extended phenotypes". Wilhelm Johannsen proposed

5893-454: The reaction catalysed, and the residues used in catalysis. The triad remains the core of the active site, but it is evolutionarily adapted to serve different functions. Some proteins, called pseudoenzymes , have non-catalytic functions (e.g. regulation by inhibitory binding) and have accumulated mutations that inactivate their catalytic triad. Catalytic triads perform covalent catalysis via an acyl-enzyme intermediate. If this intermediate

5976-428: The role of mutations in mice were studied in areas such as learning and memory , circadian rhythmicity , vision, responses to stress and response to psychostimulants . This experiment involved the progeny of mice treated with ENU , or N-ethyl-N-nitrosourea, which is a potent mutagen that causes point mutations . The mice were phenotypically screened for alterations in the different behavioral domains in order to find

6059-444: The same arrangement due to the mechanistic similarities in cysteine and serine proteolysis mechanisms. Families of cysteine proteases Families of serine proteases Threonine proteases use the amino acid threonine as their catalytic nucleophile. Unlike cysteine and serine, threonine is a secondary hydroxyl (i.e. has a methyl group). This methyl group greatly restricts the possible orientations of triad and substrate as

6142-454: The second half still covalently bound to the enzyme as an acyl-enzyme intermediate . Although general-acid catalysis for breakdown of the First and Second tetrahedral intermediate may occur by the path shown in the diagram, evidence supporting this mechanism with chymotrypsin has been controverted. The second stage of catalysis is the resolution of the acyl-enzyme intermediate by the attack of

6225-605: The slow acetylator SNPs in the coding region predominantly act through creating an unstable protein that aggregates intracellularly prior to ubiquitination and degradation. 50% of the British population are deficient in hepatic N -acetyltransferase. This is known as a negative acetylator status. Drugs affected by this are: Adverse events from this deficiency include peripheral neuropathy and hepatoxicity . The slowest acetylator haplotype , NAT2*5B (strongest association with bladder cancer ), seems to have been selected for in

6308-527: The top signal for insulin resistance , a key marker of diabetes and a major cardiovascular risk factor and has been shown to be associated with whole-body insulin resistance in NAT1 knockout mice . NAT1 is thought to have an endogenous role, likely linked to fundamental cellular metabolism. This may be related to why NAT1 is more widely distributed among tissues than NAT2. Each individual metabolizes xenobiotics at different rates, resulting from polymorphisms of

6391-451: The triad's nucleophile), catalytic triads show some of the best examples of convergent evolution . Chemical constraints on catalysis have led to the same catalytic solution independently evolving in at least 23 separate superfamilies . Their mechanism of action is consequently one of the best studied in biochemistry . The enzymes trypsin and chymotrypsin were first purified in the 1930s. A serine in each of trypsin and chymotrypsin

6474-499: The two enzymes share 75-95% of their amino acid sequence . Both also have an active site cysteine residue (Cys) in the N-terminal region. Further, all functional NAT enzymes contain a triad of catalytically essential residues made up of this cysteine , histidine , and asparagine . It has been hypothesized that the catalytic effects of the breast cancer drug Cisplatin are related to Cys. The inactivation of NAT1 by Cisplatin

6557-555: The wild-type NAT2 is classified as a fast acetylator. Slow acetylators tend to be associated with drug toxicity and cancer susceptibility. For instance, the NAT2 slow acetylator genotype is associated with an increased risk of bladder cancer , especially among cigarette smokers. Single nucleotide polymorphisms (SNPs) of NAT1 include R64W, V149I, R187Q, M205V, S214A, D251V, E26K, and I263V, and are related to genetic predisposition to cancer , birth defects , and other diseases. The effect of

6640-430: The xenobiotic metabolism genes . Both NAT1 and NAT2 are encoded by two highly polymorphic genes located on chromosome 8 . NAT2 polymorphisms were one of the first variations to explain this inter-individual variability for drug metabolism . These polymorphisms modify the stability and/ or catalytic activity of enzymes that alter acetylation rates for drugs and xenobiotics, a trait called acetylator phenotype . For NAT2,

6723-520: The α/β-hydrolase superfamily, the Ser-His-Asp triad is tuned by surrounding residues to perform at least 17 different reactions. Some of these reactions are also achieved with mechanisms that have altered formation, or resolution of the acyl-enzyme intermediate, or that don't proceed via an acyl-enzyme intermediate. Additionally, an alternative transferase mechanism has been evolved by amidophosphoribosyltransferase , which has two active sites. In

6806-405: Was first used by Davis in 1949, "We here propose the name phenome for the sum total of extragenic, non-autoreproductive portions of the cell, whether cytoplasmic or nuclear. The phenome would be the material basis of the phenotype, just as the genome is the material basis of the genotype ." Although phenome has been in use for many years, the distinction between the use of phenome and phenotype

6889-453: Was identified as the catalytic nucleophile (by diisopropyl fluorophosphate modification) in the 1950s. The structure of chymotrypsin was solved by X-ray crystallography in the 1960s, showing the orientation of the catalytic triad in the active site . Other proteases were sequenced and aligned to reveal a family of related proteases, now called the S1 family. Simultaneously, the structures of

#557442