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50-581: Cytochromes P450 ( P450s or CYPs ) are a superfamily of enzymes containing heme as a cofactor that mostly, but not exclusively, function as monooxygenases . However, they are not omnipresent; for example, they have not been found in Escherichia coli . In mammals, these enzymes oxidize steroids , fatty acids , xenobiotics , and participate in many biosyntheses. By hydroxylation, CYP450 enzymes convert xenobiotics into hydrophilic derivatives, which are more readily excreted. P450s are, in general,

100-443: A cystine unit with a disulfide bond (−S−S−). Disulfide bonds can contribute to a protein's tertiary structure if the cysteines are part of the same peptide chain, or contribute to the quaternary structure of multi-unit proteins by forming fairly strong covalent bonds between different peptide chains. A physical manifestation of cysteine-cystine equilibrium is provided by hair straightening technologies. Sulfhydryl groups in

150-400: A semiochemical , activating certain mouse olfactory sensory neurons, and attracting female mice . Copper has been shown to be required by a specific mouse olfactory receptor, MOR244-3, which is highly responsive to MTMT as well as to various other thiols and related compounds. A human olfactory receptor, OR2T11 , has been identified which, in the presence of copper, is highly responsive to

200-494: A "reverse type I" spectrum, by processes that are as yet unclear. Inhibitors and certain substrates that bind directly to the heme iron give rise to the type II difference spectrum, with a maximum at 430 nm and a minimum at 390 nm (see inset graph in figure). If no reducing equivalents are available, this complex may remain stable, allowing the degree of binding to be determined from absorbance measurements in vitro C: If carbon monoxide (CO) binds to reduced P450,

250-450: A heme-iron center. The iron is tethered to the protein via a cysteine thiolate ligand . This cysteine and several flanking residues are highly conserved in known P450s, and have the formal PROSITE signature consensus pattern [FW] - [SGNH] - x - [GD] - {F} - [RKHPT] - {P} - C - [LIVMFAP] - [GAD]. In general, the P450 catalytic cycle proceeds as follows: Mechanistic details, including

300-623: A number of routes, but the principal method is H-atom abstraction from thiols. Another method involves homolysis of organic disulfides. In biology thiyl radicals are responsible for the formation of the deoxyribonucleic acids, building blocks for DNA . This conversion is catalysed by ribonucleotide reductase (see figure). Thiyl intermediates also are produced by the oxidation of glutathione , an antioxidant in biology. Thiyl radicals (sulfur-centred) can transform to carbon-centred radicals via hydrogen atom exchange equilibria . The formation of carbon -centred radicals could lead to protein damage via

350-533: A superfamily is commonly conserved, although substrate specificity may be significantly different. Catalytic residues also tend to occur in the same order in the protein sequence. For the families within the PA clan of proteases, although there has been divergent evolution of the catalytic triad residues used to perform catalysis, all members use a similar mechanism to perform covalent, nucleophilic catalysis on proteins, peptides or amino acids. However, mechanism alone

400-451: Is conducted on a scaffold that anchors the growing chain through a thioester derived from the thiol Coenzyme A . The biosynthesis of methane , the principal hydrocarbon on Earth, arises from the reaction mediated by coenzyme M , 2-mercaptoethyl sulfonic acid. Thiolates, the conjugate bases derived from thiols, form strong complexes with many metal ions, especially those classified as soft. The stability of metal thiolates parallels that of

450-455: Is conserved through the superfamily, not even those in the catalytic triad . Conversely, the individual families that make up a superfamily are defined on the basis of their sequence alignment, for example the C04 protease family within the PA clan. Nevertheless, sequence similarity is the most commonly used form of evidence to infer relatedness, since the number of known sequences vastly outnumbers

500-424: Is currently possible. They are therefore amongst the most ancient evolutionary events currently studied. Some superfamilies have members present in all kingdoms of life , indicating that the last common ancestor of that superfamily was in the last universal common ancestor of all life (LUCA). Superfamily members may be in different species, with the ancestral protein being the form of the protein that existed in

550-441: Is illustrated by one synthesis of thioglycolic acid : Organolithium compounds and Grignard reagents react with sulfur to give the thiolates, which are readily hydrolyzed: Phenols can be converted to the thiophenols via rearrangement of their O -aryl dialkylthiocarbamates. Thiols are prepared by reductive dealkylation of sulfides, especially benzyl derivatives and thioacetals. Thiophenols are produced by S -arylation or

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600-584: Is important in nature. With metal ions, thiolates behave as ligands to form transition metal thiolate complexes . The term mercaptan is derived from the Latin mercurium captans (capturing mercury) because the thiolate group bonds so strongly with mercury compounds. According to hard/soft acid/base (HSAB) theory , sulfur is a relatively soft (polarizable) atom. This explains the tendency of thiols to bind to soft elements and ions such as mercury, lead, or cadmium. The stability of metal thiolates parallels that of

650-447: Is no minimum level of sequence similarity guaranteed to produce identical structures. Over long periods of evolution, related proteins may show no detectable sequence similarity to one another. Sequences with many insertions and deletions can also sometimes be difficult to align and so identify the homologous sequence regions. In the PA clan of proteases , for example, not a single residue

700-445: Is not sufficient to infer relatedness. Some catalytic mechanisms have been convergently evolved multiple times independently, and so form separate superfamilies, and in some superfamilies display a range of different (though often chemically similar) mechanisms. Protein superfamilies represent the current limits of our ability to identify common ancestry. They are the largest evolutionary grouping based on direct evidence that

750-400: Is referred to as either a thiol group or a sulfhydryl group , or a sulfanyl group . Thiols are the sulfur analogue of alcohols (that is, sulfur takes the place of oxygen in the hydroxyl ( −OH ) group of an alcohol), and the word is a blend of " thio- " with "alcohol". Many thiols have strong odors resembling that of garlic or rotten eggs. Thiols are used as odorants to assist in

800-515: Is the gene that encodes the enzyme CYP2E1 —one of the enzymes involved in paracetamol (acetaminophen) metabolism. The CYP nomenclature is the official naming convention, although occasionally CYP450 or CYP 450 is used synonymously. These names should never be used as according to the nomenclature convention (as they denote a P450 in family number 450). However, some gene or enzyme names for P450s are also referred to by historical names (e.g. P450 BM3 for CYP102A1) or functional names, denoting

850-579: Is typically more conserved than DNA sequence (due to the degenerate genetic code ), so it is a more sensitive detection method. Since some of the amino acids have similar properties (e.g., charge, hydrophobicity, size), conservative mutations that interchange them are often neutral to function. The most conserved sequence regions of a protein often correspond to functionally important regions like catalytic sites and binding sites, since these regions are less tolerant to sequence changes. Using sequence similarity to infer homology has several limitations. There

900-537: Is used to destroy the odor. A copper-based oxidation catalyst neutralizes the volatile thiols and transforms them into inert products. Thiols show little association by hydrogen bonding , both with water molecules and among themselves. Hence, they have lower boiling points and are less soluble in water and other polar solvents than alcohols of similar molecular weight. For this reason also, thiols and their corresponding sulfide functional group isomers have similar solubility characteristics and boiling points, whereas

950-533: Is very rare to find “consistently isolated superfamilies”. When domains do combine, the N- to C-terminal domain order (the "domain architecture") is typically well conserved. Additionally, the number of domain combinations seen in nature is small compared to the number of possibilities, suggesting that selection acts on all combinations. Several biological databases document protein superfamilies and protein folds, for example: Similarly there are algorithms that search

1000-448: The D 2 O -exchangeable S H signal in the H NMR spectrum ( S is NMR -active but signals for divalent sulfur are very broad and of little utility ). The ν SH band appears near 2400 cm in the IR spectrum . In the nitroprusside reaction , free thiol groups react with sodium nitroprusside and ammonium hydroxide to give a red colour. In industry, methanethiol is prepared by

1050-456: The PDB for proteins with structural homology to a target structure, for example: Thiolate In organic chemistry , a thiol ( / ˈ θ aɪ ɒ l / ; from Ancient Greek θεῖον (theion)  ' sulfur ' ), or thiol derivative , is any organosulfur compound of the form R−SH , where R represents an alkyl or other organic substituent . The −SH functional group itself

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1100-848: The Wayback Machine ) and allele names ( CYP Allele Nomenclature Committee ). Based on the nature of the electron transfer proteins, P450s can be classified into several groups: The most common reaction catalyzed by cytochromes P450 is a monooxygenase reaction, e.g., insertion of one atom of oxygen into the aliphatic position of an organic substrate (RH), while the other oxygen atom is reduced to water: Many hydroxylation reactions (insertion of hydroxyl groups) use CYP enzymes, but many other hydroxylases exist. Alpha-ketoglutarate-dependent hydroxylases also rely on an Fe=O intermediate but lack hemes. Methane monooxygenase, which converts methane to methanol, are non-heme iron-and iron-copper-based enzymes. The active site of cytochrome P450 contains

1150-405: The active site of an enzyme can form noncovalent bonds with the enzyme's substrate as well, contributing to covalent catalytic activity in catalytic triads . Active site cysteine residues are the functional unit in cysteine protease catalytic triads . Cysteine residues may also react with heavy metal ions (Zn , Cd , Pb , Hg , Ag ) because of the high affinity between the soft sulfide and

1200-407: The iron (and eventually molecular oxygen ). Genes encoding P450 enzymes, and the enzymes themselves, are designated with the root symbol CYP for the superfamily , followed by a number indicating the gene family , a capital letter indicating the subfamily, and another numeral for the individual gene. The convention is to italicize the name when referring to the gene. For example, CYP2E1

1250-479: The oxygen rebound mechanism , have been investigated with synthetic analogues, consisting of iron oxo heme complexes. Binding of substrate is reflected in the spectral properties of the enzyme, with an increase in absorbance at 390 nm and a decrease at 420 nm. This can be measured by difference spectroscopies and is referred to as the "type I" difference spectrum (see inset graph in figure). Some substrates cause an opposite change in spectral properties,

1300-487: The thiolate group ( RS ) bonds very strongly with mercury compounds. Thiols having the structure R−SH, in which an alkyl group (R) is attached to a sulfhydryl group (SH), are referred to as alkanethiols or alkyl thiols . Thiols and alcohols have similar connectivity. Because sulfur atoms are larger than oxygen atoms, C−S bond lengths – typically around 180 picometres – are about 40 picometers longer than typical C−O bonds. The C−S−H angles approach 90° whereas

1350-687: The BDE is 440 kJ/mol (110 kcal/mol). An S−H bond is moderately polar because of the small difference in the electronegativity of sulfur and hydrogen. In contrast, O−H bonds in hydroxyl groups are more polar. Thiols have a lower dipole moment relative to their corresponding alcohols. There are several ways to name the alkylthiols: Many thiols have strong odors resembling that of garlic . The odors of thiols, particularly those of low molecular weight, are often strong and repulsive. The spray of skunks consists mainly of low-molecular-weight thiols and derivatives. These compounds are detectable by

1400-411: The alcohols, thiols are more acidic. The conjugate base of a thiol is called a thiolate . Butanethiol has a p K a of 10.5 vs 15 for butanol. Thiophenol has a p K a of 6, versus 10 for phenol . A highly acidic thiol is pentafluorothiophenol (C 6 F 5 SH) with a p K a of 2.68. Thus, thiolates can be obtained from thiols by treatment with alkali metal hydroxides. Thiols, especially in

1450-432: The alkylation of sodium hydrosulfide . This method is used for the production of thioglycolic acid from chloroacetic acid . In general, on the typical laboratory scale, the direct reaction of a haloalkane with sodium hydrosulfide is in efficient owing to the competing formation of sulfides. Instead, alkyl halides are converted to thiols via an S -alkylation of thiourea . This multistep, one-pot process proceeds via

1500-438: The ancestral species ( orthology ). Conversely, the proteins may be in the same species, but evolved from a single protein whose gene was duplicated in the genome ( paralogy ). A majority of proteins contain multiple domains. Between 66-80% of eukaryotic proteins have multiple domains while about 40-60% of prokaryotic proteins have multiple domains. Over time, many of the superfamilies of domains have mixed together. In fact, it

1550-543: The angle for the C−O−H group is more obtuse. In solids and liquids, the hydrogen-bonding between individual thiol groups is weak, the main cohesive force being Van der Waals interactions between the highly polarizable divalent sulfur centers. The S−H bond is much weaker than the O−H bond as reflected in their respective bond dissociation energies (BDE). For CH 3 S−H, the BDE is 366 kJ/mol (87 kcal/mol), while for CH 3 O−H,

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1600-486: The aroma of roasted coffee , whereas grapefruit mercaptan , a monoterpenoid thiol, is responsible for the characteristic scent of grapefruit . The effect of the latter compound is present only at low concentrations. The pure mercaptan has an unpleasant odor. In the United States, natural gas distributors were required to add thiols, originally ethanethiol , to natural gas (which is naturally odorless) after

1650-669: The catalytic activity and the name of the compound used as substrate. Examples include CYP5A1 , thromboxane A 2 synthase, abbreviated to TBXAS1 ( T hrom B o X ane A 2 S ynthase 1 ), and CYP51A1 , lanosterol 14-α-demethylase, sometimes unofficially abbreviated to LDM according to its substrate ( L anosterol) and activity ( D e M ethylation). The current nomenclature guidelines suggest that members of new CYP families share at least 40% amino-acid identity, while members of subfamilies must share at least 55% amino-acid identity. Nomenclature committees assign and track both base gene names ( Cytochrome P450 Homepage Archived 2010-06-27 at

1700-500: The catalytic cycle is interrupted. This reaction yields the classic CO difference spectrum with a maximum at 450 nm. However, the interruptive and inhibitory effects of CO varies upon different CYPs such that the CYP3A family is relatively less affected. Protein superfamily Superfamilies of proteins are identified using a number of methods. Closely related members can be identified by different methods to those needed to group

1750-399: The corresponding sulfide minerals. Thiolates react with carbon disulfide to give thioxanthate ( RSCS 2 ). Free radicals derived from mercaptans, called thiyl radicals , are commonly invoked to explain reactions in organic chemistry and biochemistry . They have the formula RS where R is an organic substituent such as alkyl or aryl . They arise from or can be generated by

1800-553: The deadly New London School explosion in New London, Texas , in 1937. Many gas distributors were odorizing gas prior to this event. Most currently-used gas odorants contain mixtures of mercaptans and sulfides, with t -butyl mercaptan as the main odor constituent in natural gas and ethanethiol in liquefied petroleum gas (LPG, propane). In situations where thiols are used in commercial industry, such as liquid petroleum gas tankers and bulk handling systems, an oxidizing catalyst

1850-408: The detection of natural gas (which in pure form is odorless), and the "smell of natural gas" is due to the smell of the thiol used as the odorant. Thiols are sometimes referred to as mercaptans ( / m ər ˈ k æ p t æ n / ) or mercapto compounds , a term introduced in 1832 by William Christopher Zeise and is derived from the Latin mercurio captāns ('capturing mercury') because

1900-502: The formation of C −C bonds or backbone fragmentation. Because of the weakness of the S−H bond, thiols can function as scavengers of free radicals . As the functional group of the amino acid cysteine , the thiol group plays a very important role in biology. When the thiol groups of two cysteine residues (as in monomers or constituent units) are brought near each other in the course of protein folding, an oxidation reaction can generate

1950-512: The gas odorants (see below) ethanethiol and t -butyl mercaptan as well as other low molecular weight thiols, including allyl mercaptan found in human garlic breath, and the strong-smelling cyclic sulfide thietane . Thiols are also responsible for a class of wine faults caused by an unintended reaction between sulfur and yeast and the "skunky" odor of beer that has been exposed to ultraviolet light. Not all thiols have unpleasant odors. For example, furan-2-ylmethanethiol contributes to

2000-426: The human nose at concentrations of only 10 parts per billion. Human sweat contains ( R )/( S )-3-methyl-3-mercapto-1-ol (MSH), detectable at 2 parts per billion and having a fruity, onion -like odor. (Methylthio)methanethiol (MeSCH 2 SH; MTMT) is a strong-smelling volatile thiol, also detectable at parts per billion levels, found in male mouse urine. Lawrence C. Katz and co-workers showed that MTMT functioned as

2050-454: The intermediacy of the isothiouronium salt , which is hydrolyzed in a separate step: The thiourea route works well with primary halides, especially activated ones. Secondary and tertiary thiols are less easily prepared. Secondary thiols can be prepared from the ketone via the corresponding dithioketals . A related two-step process involves alkylation of thiosulfate to give the thiosulfonate (" Bunte salt "), followed by hydrolysis. The method

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2100-402: The most evolutionarily divergent members. Historically, the similarity of different amino acid sequences has been the most common method of inferring homology . Sequence similarity is considered a good predictor of relatedness, since similar sequences are more likely the result of gene duplication and divergent evolution , rather than the result of convergent evolution . Amino acid sequence

2150-597: The number of known tertiary structures . In the absence of structural information, sequence similarity constrains the limits of which proteins can be assigned to a superfamily. Structure is much more evolutionarily conserved than sequence, such that proteins with highly similar structures can have entirely different sequences. Over very long evolutionary timescales, very few residues show detectable amino acid sequence conservation, however secondary structural elements and tertiary structural motifs are highly conserved. Some protein dynamics and conformational changes of

2200-405: The presence of base, are readily oxidized by reagents such as bromine and iodine to give an organic disulfide (R−S−S−R). Oxidation by more powerful reagents such as sodium hypochlorite or hydrogen peroxide can also yield sulfonic acids (RSO 3 H). Oxidation can also be effected by oxygen in the presence of catalysts: Thiols participate in thiol-disulfide exchange: This reaction

2250-563: The protein structure may also be conserved, as is seen in the serpin superfamily . Consequently, protein tertiary structure can be used to detect homology between proteins even when no evidence of relatedness remains in their sequences. Structural alignment programs, such as DALI , use the 3D structure of a protein of interest to find proteins with similar folds. However, on rare occasions, related proteins may evolve to be structurally dissimilar and relatedness can only be inferred by other methods. The catalytic mechanism of enzymes within

2300-500: The reaction of hydrogen sulfide with methanol . This method is employed for the industrial synthesis of methanethiol : Such reactions are conducted in the presence of acidic catalysts. The other principal route to thiols involves the addition of hydrogen sulfide to alkenes . Such reactions are usually conducted in the presence of an acid catalyst or UV light. Halide displacement, using the suitable organic halide and sodium hydrogen sulfide has also been used. Another method entails

2350-565: The replacement of diazonium leaving group with sulfhydryl anion (SH ): Akin to the chemistry of alcohols, thiols form sulfides , thioacetals , and thioesters , which are analogous to ethers , acetals , and esters respectively. Thiols and alcohols are also very different in their reactivity, thiols being more easily oxidized than alcohols. Thiolates are more potent nucleophiles than the corresponding alkoxides . Thiols, or more specific their conjugate bases, are readily alkylated to give sulfides: Thiols are easily deprotonated. Relative to

2400-558: The same is not true of alcohols and their corresponding isomeric ethers. The S−H bond in thiols is weak compared to the O−H bond in alcohols. For CH 3 X−H, the bond enthalpies are 365.07 ± 2.1 kcal/mol for X = S and 440.2 ± 3.0 kcal/mol for X = O. Hydrogen-atom abstraction from a thiol gives a thiyl radical with the formula RS , where R = alkyl or aryl. Volatile thiols are easily and almost unerringly detected by their distinctive odor. Sulfur-specific analyzers for gas chromatographs are useful. Spectroscopic indicators are

2450-471: The soft metal (see hard and soft acids and bases ). This can deform and inactivate the protein, and is one mechanism of heavy metal poisoning . Drugs containing thiol group 6-Mercaptopurine (anticancer) Captopril (antihypertensive) D-penicillamine (antiarthritic) Sodium aurothiolate (antiarthritic) Many cofactors (non-protein-based helper molecules) feature thiols. The biosynthesis and degradation of fatty acids and related long-chain hydrocarbons

2500-403: The terminal oxidase enzymes in electron transfer chains, broadly categorized as P450-containing systems . The term "P450" is derived from the spectrophotometric peak at the wavelength of the absorption maximum of the enzyme (450  nm ) when it is in the reduced state and complexed with carbon monoxide . Most P450s require a protein partner to deliver one or more electrons to reduce

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