Intradiol dioxygenases from various microorganisms
Aromatic compounds are derived from both natural and anthropogenic sources. Under natural conditions, arenes are formed as a result of the pyrolysis of organic materials at high temperatures during forest, steppe and peatland fires, and during volcanic eruptions. Biogenic aromatic compounds like aromatic amino acids and lignin, the second most abundant organic compound in the environment, are universally distributed in nature. Many species of plants, especially willow (
Due to the delocalization of π orbitals aromatic compounds are very stable . For many years it has been searching for microorganism able to breakdown these kind of substrates. Among the bacteria, representatives of the genus
The strategy for degradation of aromatic structure comprises hydroxylation and cleavage of the aromatic ring with the usage of oxygenases [8,23,24]. These reactions are initiated by electrophilic attack of molecular oxygen and they are retarded by the presence of electron-withdrawing substituents. For this reason the velocity of reaction is connected with the kind of substituents in the aromatic ring. Substituents of the first group such as: -NH2, -OH, -OCH3, -CH3, -C6H5 activate aromatic ring for electrophilic attack. In contrary, the substituents of the second group (-NO2, -N(CH3)3+, -CN, -COOH, -COOR, -SO3H, -CHO, -COR) and the third group (-F, -Cl, -Br, -I) impede the electrophilic attack by dioxygenases [3,25-28].
Hydroxylation into the dihydroxylated intermediates, the first step in the oxidative degradation of aromatic compounds, is catalyzed by monooxygenases or hydroxylating dioxygenases (Fig. 1). Aromatic monooxygenases are divided into two groups: activated- ring monooxygenases and nonactivated- ring enzymes and usually contain FAD as a prosthetic group. These enzymes posses a dinuclear iron centre with two oxo- bridged iron atoms (Fe-O-Fe) in the active site [36-39]. Aromatic monooxygenases activate molecular oxygen through the formation of a reactive flavin (hydro)peroxide which can attack the substrate [31,33-35].
Aromatic ring hydroxylating dioxygenases that belong to the Rieske non-heme iron oxygenases are multicomponent enzyme systems. The reaction catalyzed by hydroxylating dioxygenases requires two electrons from a NAD(P)H that are consecutively transferred to the terminal oxygenase component through a electron carries such as ferredoxin and/or a reductase .
As a result of hydroxylation key intermediates such as catechol, protocatechuic acid, hydroxyquinol, or gentisic acid are formed. These products are substrates for ring-cleaving dioxygenases [17,37-39]. The ring-cleaving dioxygenases couple O2 bond cleavage with ring fission of hydroxylated derivatives either between the two hydroxyl group (
Intradiol dioxygenases catalyze the intradiol cleavage of the aromatic ring at 1,2-position of catechol or its derivatives (protocatechuic acid, hydroxyquinol) with incorporation of two atoms of molecular oxygen into the substrate. It leads to the production of
Extradiol catechol and protocatechuate dioxygenases catalyze the ring fission between position C2 and C3 of catechol ring and between position C2 and C4 or C4 and C5 of protocatechuate ring respectively. Products of these reactions (2-hydroxymuconic semialdehyde or carboxy-2-hydroxymuconic semialdehyde) are transformed finally to pyruvic acid and acetaldehyde in catechol pathway and pyruvic acid and acetaldehyde or pyruvic acid and oxaloacetic acid in protocatechuate pathway (Fig. 1) [37,43].
Degradation of aromatic compounds by the
Because some aromatics have been present in the environment for a very short time, bacteria have not evolved efficient pathways for their degradation and for that reason the construction of such pathways may be required. Therefore, a detailed understanding of the molecular bases as well as enzymes of known pathways is essential .
Our chapter is divided into three parts: first we classify bacterial intradiol dioxygenases, key enzymes in aromatic compounds degradation, taking under consideration phylogenetic relationships among dioxygenases from various strains and their substrate specificity. Next, we present current knowledge about molecular structure of these dioxygenases and hypothetical mechanisms for aromatic ring cleavage. And finally, we describe modifications increasing biodegradation potential of these enzymes.
2. Classification of bacterial intradiol dioxygenases
Many studies on intradiol dioxygenases concentrate on the understanding of their biochemical and structural properties. Based on the results of these studies and taking into consideration substrate specificity of the
Although Murakami et al.  observed partial activity of hydroxyquinol 1,2-dioxygenase towards catechol and Pandeeti and Siddavattam  isolated catechol 1,2-dioxygenase which was active strictly against catechol and 1,2,3-benzenotriol there is no reports about activity of catechol 1,2-dioxygenases towards hydroxyquinol [18,21,50,51]. Therefore, we propose to divide the intradiol dioxygenases into three classes: catechol 1,2-dioxygenases, protocatechuate 3,4-dioxygenases, and hydroxyquinol 1,2-dioxygenases. Representatives of these three classes are presented in Table 1. Based on the results of biochemical and genetic comparison of intradiol dioxygenases Perez-Pantoja et al.  distinguished hydroxyquinol 1,2-dioxygenases as a separate cluster that may support our suggestions.
The catechol 1,2-dioxygenases family can be divided into several subclasses depending on their substrate specificity. Initially this family was divided into two subclasses: type I dioxygenases with activity against catechol and lack or weak activity against chlorocatechol and type II dioxygenases, which cleave only chlorocatechols . Then, based on their amino acid sequences Liu et al.  divided family of catechol 1,2-dioxygenases into three groups: catechol 1,2-dioxygenases from gram-negative bacteria, chlorocatechol 1,2-dioxygenases from gram-negative bacteria, and both catechol- and chlorocatechol 1,2-dioxygenases from gram-positive bacteria. However, both of these classifications do not take into consideration substrate specificity of these enzymes towards methylcatechols. High substrate specificity against these compounds was observed for intradiol dioxygenase isolated from genus
3. Molecular structure and reaction mechanism of intradiol dioxygenases
Intradiol dioxygenases belong to metalloenzymes with non-heme iron (III) that plays a crucial role for the binding and activation of dioxygen in the cleavage reaction [55,59]. Metal ion is ligated by two tyrosine and two histidine residues that are highly conserved in all investigated intradiol dioxygenases. The fifth ligand is a hydroxyl group derived from the solvent.
Two structurally different intradiol dioxygenases families can be singled out: catechol/hydroxyquinol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases. Catechol/hydroxyquinol 1,2-dioxygenases are dimmers (αFe3+)2 with identical or similar subunits while protocatechuate 3,4-dioxygenases are typically composed of two homologous subunits in oligomeric complexes (αβFe3+)2-12  (Fig. 3).
3.1. Catechol 1,2-dioxygenases characterization
Catechol 1,2-dioxygenases catalyze cleavage of catechol and its derivatives. The tertiary structure of the enzymes from this class is similar [53,59,61,64,66]. They form homodimers with two subunits connected with helical zipper motif. Each subunit has a molecular mass of 29.0-38.6 kDa.
Subunits of catechol 1,2-dioxygenases contain two molecules of phospholipids bound into a hydrophobic cavity at the dimeric interface [38,47,49,50,53,59,61,64,66,67]. On the base of electron density and the stereochemistry these phospholipids were identified as a phosphatidylcholine with two C14-15/C12-C17 hydrophobic tails . It is suggested that the phospholipid chains may modulate the activity of catechol 1,2-dioxygenases by increasing the local concentration of substrate or the lipids act as an effector molecule. The binding of phospholipid to hydrophobic amino acid of the active site can lead to a conformational change at this place. During catalysis catechol is cleaved to
Unique helical N-terminal domain was first described by Vetting and Ohlendorf  for catechol 1,2-dioxygenase from
Catechol 1,2-dioxygenase from
The linker domain of catechol 1,2-dioxygenases contains 12 α helices. Five of them belong to the N-terminal chain of each monomer and one extending from each catalytic domain. The active site with ferric ion is located between β sheets sandwich and the linker domain . Matera et. al.  compared structure of catechol 1,2-dioxygenase from Gram- positive strain
As it was mentioned earlier the metal ion is ligated by four amino acid residues and a hydroxyl group from water in trigonal bipyramidal geometry. One molecule of tyrosine and one histidine are the axial ligands, whereas the second Tyr, His and a solvent molecule make up the equatorial plane. [38,47,50,53]. Since the two Fe3+ ions from catalytic domains are separated by more than 40 Å Vetting and Ohlendorf  suggested that they act structurally and catalytically independently. It explains the lack of allosteric effect [25,46,57,59,61,70,80]. However, catechol 1,2-dioxygenase from
The substrate specificity of catechol 1,2-dioxygenases depends on electronic factors, which can play a significant role in determining the efficiency of conversion of catechol derivatives. Currently, there is little information about the influence of steric factors on catalytic properties of catechol 1,2-dioxygenases . Sauret-Ignazi et al. revealed that very high inhibition constant is connected with steric hindrance, for example by methoxyl group. However another studies have indicated that a steric hindrances are not determining the rate-limiting step but there is a strong correlation between substituent electronegativity and kcat [25,50,61].
The catalytic cycle of catechol 1,2-dioxygenases involve binding of the catechol or its derivatives as a dianion with simultaneous dissociation of one tyrosine and water molecule (a-e). One hydroxyl group of substrate binds in an axial position
In the first case, proton remains in the active site (i) and the peroxide oxygen atom is protonated. It prevents oxidation of iron to a high-valent Fe(IV)=O state during the O-O bond cleavage. As a result peroxide ligand undergoes a Criegee rearrangement with O-O bond heterolysis and migration of the acyl group to the peroxide oxygen (k). It is also possible that the peroxide ligand converts to muconic anhydrate product via O-O bond cleavage made easier by the equatorial tyrosine, which is oxidized to a tyrozyl radical (j). The reduction of tyrozyl radical to tyrosinate is connected with the oxyl radical attack on the carbonyl carbon .
In the second case, proton is released from the active site (n) and peroxide bridge is cleaved to reactive oxoferryl group and an alkoxyl radical (o). Alkoxyl radical attacks the adjacent carbonyl carbon, followed by the ring expansion and protonation of the oxo ligand leads to the cyclic anhydride (k). Hydrolysis of the anhydride leads to the final reaction product – muconic acid (l,m) (Fig. 3) [40,92].
The electrophilic attack of molecular oxygen on iron (III)-bound catecholate is judged to be an essential step in the catalytic reaction of catechol 1,2-dioxygenase . For this type of chemical reaction the σ-complex is assumed to be next to the transition state. The formation of σ-complex requires the highest free energy of activation and must consequently be rate-limiting .
Sauret-Ignazi et al.  observed that monophenolic compounds are also bound by enzyme and they suggested that only one deprotonated hydroxyl may be sufficient for binding of the substrate to the active site.
Matera et al.  calculated parameter for nucleophilic reactivity for catechol, 3-chloro-, 4-chloro-, 3-methyl-, 4-methylcatechols, and pyrogallol. They revealed that the interaction between the frontier orbitals, the highest occupied molecular orbital (HOMO) of nucleophiles (catechols) and the lowest unoccupied molecular orbital (LUMO) of electrophile (the active site iron ion), is essential and lowers the activation barrier. Since the nuclephilic attack of the aromatic π electrons of the iron(III)-bound catecholate on the oxygen molecule is an important step in the cleavage reaction, the HOMO of the catecholate is assumed to be the relevant frontier orbital. The natural logarithm of the kcat is proportional to the activation energy of the rate-limiting step and is correlated to the energy of HOMO .
The main interaction of catechol 1,2-dioxygenase from
Catechol derivatives with the substituents on the C3 position can be bound in two different orientations in the enzyme active site from ADP1 strain. The substituent may be located in a pocket created by residues Ile105, Pro108, His226, Gln240 and Arg221 or its positioning may lead to a steric conflict with Tyr200. However, rearrangement in the active site makes possible the interaction of substituent on C3 with the π electrons of Tyr200 . According to Matera et al.  the lower affinity of catechol 1,2-dioxygenase from 1CP strain for 3-substituents results from the lack of Tyr106. Tyr 196 is not connected then and it can cause the more open conformation of the space to the 3-substituent binding. It influences a certain degree of disorder in substrates binding to the iron and/or a not suitable coordination for productive conversion.
Ferraroni et al.  showed that preference of chlorocatechol dioxygenases for 3-chlorocatechol is connected with Val53 and Tyr78 residues whereas 4-chlorocatechols are cleaved by dioxygenases with Leu and Ile at 49 and 74 position respectively. Moreover, cysteine residues are important for interacting with chlorine substituents.
Presence of large substituents makes impossible active binding of the aromatic substrates to the active site because they interact unfavorably with Pro76, Leu73 and Ile105. Vetting and Ohlendorf  suggest that catechol derivatives are ligated the iron through only one of the hydroxyl group or they are trapped in an initial binding state.
3.2. Hydroxyquinol 1,2-dioxygenases characterization
Hydroxyquinol 1,2-dioxygenases have very similar structure and reaction mechanism to catechol 1,2-dioxygenases. They form homodimers with molecular weight of 58-85 kDa. The iron (III) is coordinated by two molecules of tyrosine, two molecules of histidine and one molecule of water [17,41,84-86,90].
However, Ferraroni et al.  revealed that His42 from H2 helix of the linker domain is connected with the copper ion in an oxidation state of +1. Probably it plays a role in stabilization of the enzyme quaternary structure. Moreover, a few different amino acid residues of hydroxyquinol 1,2-dioxygenases responsible for substrate selection were selected: Leu80, Asp83, Val107, Phe108, Gly109, Pro110, Phe111, Ile199, Pro200, Arg218, and Val251 .
One of the most characteristic feature of hydroxyquinol 1,2-dioxygenases is the extensive opening of the upper part of catalytic cavity which is responsible for favorable binding of hydroxyquinol [17,83]. Zaborina et al.  connected this fact with lower activation energy. Catalytic process of
3.3. Protocatechuate 3,4-dioxygenases characterization
Protocatechuate 3,4-dioxygenases catalyze cleavage of protocatechuic acid and its derivatives. The mechanism of this reaction is the same as intradiol fission of catechol ring [13,92]. During substrate binding as a dianion to the active site of the enzyme the axial tyrosine is dissociated from the iron(III). It causes conformational changes that yields the chelated iron(III)-protocatechuate complex. Vetting et al.  suggested that the function of the structural rearrangements would be to facilitate the reaction of oxygen with the substrate. Electron transfer from the substrate to dioxygen aids a binding of dioxygen to the iron(III). The activation of substrate for an electrophilic attack by dioxygen leads to the formation of a peroxo bridge between the iron and C4 of substrate. O-O bond cleavage occurs after acyl migration to the peroxo oxygen. It leads to the cyclic anhydride formation and its hydrolysis to the final acyclic product [16,80,92,93].
Although protocatechuate 3,4-dioxygenases are heterodimers with molecular mass of 97.0-700.0 kDa [12,18,72,75,82] theirs tertiary structure is similar to the enzymes from catechol 1,2-dioxygenase family. Protocatechuate 3,4-dioxygenases belong to the non-heme iron dioxygenases and are composed of equimolar amounts of two different α and β subunits [11,68,78,82,93]. These enzymes have a tetrahedral shape with α subunit forming the apex of the tetrahedron. The central cavity is accessible to solvent through triangular channels. A number of basic residues (mainly arginine and lysine) line the entrance to the active site of the enzyme producing regions of positive electrostatic potential. It is possible that these residues funnel the negatively charged substrate into the active site .
α and β subunits have similar folds. The core of each subunit contains two four-strand β-sheets that form a β sandwich. One β sheet consists of antiparallel strands, whereas the other has a mixed topology. The core structure is surrounded by series of small helices and large irregular loops. Two β sheets form a part of the interface between the subunits, with surrounding loops providing the remaining contacts. The amino terminus of the α subunit passes completely through a gap between the core β sandwich, supports structure of the β subunit and makes up one wall of the active-site cavity .
Aligments of the structure and sequences of α- and β-chain of protocatechuate 3,4-dioxygenases from more than 26 bacterial strains revealed that the β-chain show higher sequence identities than the α-chain. It may be connected with the fact that β-chain provides most of the active site . However, amino acids from α-subunit may interact with substrate and in this way stabilize it in the active site. Harnett et al.  observed that Arg-133 from α-subunit participates in forming ionic bond with carboxyl group of protocatechuic acid.
Protocatechuate 3,4-dioxygenases from different bacterial strains are consist of variable number of αβ protomers (2 – 12) and each protomer has a cylindrical shape [12,16,78]. The minimal catalytic unit of all protocatechuate 3,4-dioxygenases is an αβFe3+ structure, but (αβ)2Fe3+ structure has been also reported [11,72]. The crystal structure of these enzymes shows that the high-spin iron(III) is bound to the active site in a distorted trigonal bipyramidal coordination geometry with two inequivalent tyrosine ligands, two histidines, and exogenous hydroxide ion [68,69,73,77,79,92,93]. Kurahashi et al.  proposed that the electronic effect of the water ligand in the active site of protocatechuate 3,4-dioxygenase controls not only the distorted trigonal-bipyramidal structure but also plays a role in the oxidation of substrate. The two tyrosine ligands are thought to stabilize the ferric ion and give protocatechuate 3,4-dioxygenase its characteristic burgundy-red color via tyrosinate ligand–to-metal charge transfer [13,79].
Orville et al.  demonstrated that at least two iron binding sites can be occupied by exogenous ligand such as substrates, analog of substrate, and small molecules. It leads to the dynamic changes in the iron coordination sphere or the orientation of the aromatic substrate and influences the catalytic cycle. An external ligand with a higher position in the spectrochemical series (Cl«RO<H2O) induces a larger degree of distortion [80,93].
The protocatechuate 3,4-dioxygenases show a high similarity not only for the ligands of the active site but also for the whole pocket in which the iron complex is located .
Orville et al.  studied cleavage mechanism in the presence of inhibitors. They proposed three different orientations of inhibitors in the active site. First, in which inhibitor protrudes out of the active site cavity but still coordinates the iron to yield trigonal bipyramidal coordination geometry. Second, in which inhibitor binds within the active site that is sufficient to dissociate the active site solvent molecules but without direct coordination to the iron. Third, in which inhibitor is completely bound within the active site, directly coordinates the iron, and yields octahedral geometry.
Many protocatechuate dioxygenases have narrow substrate specificities and regioselectivities [9,10,12]. Hou et al.  suggested that free sulfhydryl groups located at or near the active center are responsible for substrate specificity of the enzyme. It was showed that protocatechuic acid derivatives are cleaved much slower than protocatechuic acid. Transient kinetic results suggest that slower fission is probably connected with the reduced rates for substrate association and product release rather than the ring opening reaction .
4. Application of intradiol dioxygenases in bioremediation
Bioremediation is an effective treatment process that use organisms through their enzymatic activities. However, slow growth of microorganisms or difficulties in the control and maintain the optimal conditions for the microbial growth are disadvantages of biodegradation processes. The direct application of enzymes in the environmental treatment processes has been quite limited due to the loss of enzyme activity  and therefore, novel methods of enzyme stabilization are developed. One of them is immobilization which has been used as a tool to improve many of enzyme properties such as operational stability, inhibitor resistance and performance in organic solvents [95,96]. Kalogeris et al.  showed that immobilization of catechol 1,2-dioxygenase improved its performance at higher temperatures. It extended catechol 1,2-dioxygenase storage stability and retained its activity after operation cycles - properties which are fundamental for continuous bioprocesses during removal of toxic pollutants. Catechol 1,2-dioxygenase from
Immobilized intradiol dioxygenases can also be used as biosensors because of increased interest in the detection of aromatic compounds. Zucolotto et al.  successfully fabricated biosensor for catechol detection. Chlorocatechol 1,2-dioxygenase was immobilized in nanostructured films in conjuction with poly(amidoamine) dendrimer in a layer-by-layer fashion. Chlorocatechol 1,2-dioxygenase remained active on these films for longer than three weeks. Moreover, this biosensor was able to detect catechol at concentration even 10-10 M .
Polychlorinated phenols, amino- and nitrophenols have become widespread environmental pollutants because of their resistance to microbial degradation and their broad toxicity. During their degradation hydroxyquinol as a key intermediate is frequently formed. Therefore, it is believed that hydroxyquinol-metabolized enzymes play an important role in the microbial degradation of various aromatic xenobiotics [51,85,88]. Immobilization of hydroxyquinol 1,2-dioxygenase from
The important properties of degradation enzymes is a resistance to inhibitors such as metal ions, alcohols, chelators, hydrocarbons, phenols and other [58,59,61]. Metal ions can lead to the conformational changes in the enzymes such as a reduction in α-helices and β sheets, which can result in the loss of enzymatic activity  or replacement of the original metal ion at the active site of the enzymes with other metal. It may modulate their activities in accordance with the Irving-Williams studies on the stability of the metal complexes . Moreover, the thiol groups of enzyme structure may bind transition metals that can deactivate the enzyme.
Gou et al.  observed that activity of catechol 1,2-dioxygenase from
Some catechol 1,2-dioxgenases can be inhibited by chelating agent, especially by tiron – ferric ion chelating agent . However, catechol 1,2-dioxygenase from
The wide substrate specificity and inhibitor resistance of some intradiol dioxygenases makes them an attractive target in the design of enzyme systems for bioremediation.
Intradiol dioxygenases are responsible for aromatic ring cleavage and for that reason are directly involved in biogeochemical cycles, and can be very useful in the development of bioremediation technology. These enzymes are the members of the aromatic-ring-cleavage dioxygenase superfamily. Based on their substrate specificity intradiol dioxygenases could be divided into three classes: catechol 1,2-dioxygenases, protocatechuate 3,4-dioxygenases, and hydroxyquinol 1,2-dioxygenase. The mechanism of intradiol fisson is common for enzymes from all clasess. In this mechanism the high-spin iron(III) is ligated by two tyrosines, two histidines, and a water ligand in trigonal bipyramidal geometry. The catalytic cycle of the intradiol dioxygenases involve binding of the catechol as a dianion and dioxygen to the metal. It leads to the formation of a peroxo bridge between iron and C4 of substrate. In the next step the Criegee rearrangement and O-O bond cleavage occurs, leading to the cyclic anhydride formation. Hydrolysis of the anhydride leads to the formation of the final acyclic product. Structural analysis of many of intradiol dioxygenases revealed only small differences in their active site structure. However, these differences significantly influence the substrate specificity and the resistance of the enzymes to the changing environmental factors.
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