aromatic

aromatic compound

Any of a large class of organic compounds whose molecular structure includes one or more planar rings of atoms, usually but not always six carbon atoms. The ring's carbon-carbon bonds (see bonding) are neither single nor double but a type characteristic of these compounds, in which electrons are shared equally with all the atoms around the ring in an electron cloud. The term was first applied circa 1860 to a class of hydrocarbons isolated from coal tar and distinguished by odours much stronger than those of other classes of hydrocarbons. In modern chemistry, aromaticity denotes the chemical behaviour, especially the low reactivity, of this class of molecules related to their bonding. The parent compound of this class is benzene (C6H6). Seealso hydrogenation.

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Aromatic-ring-hydroxylating dioxygenases (ARHD) incorporate two atoms of dioxygen (O2) into their substrates in the dihydroxylation reaction. The product is (substituted) cis-1,2-dihydroxycyclohexadiene, which is subsequently converted to (substituted) benzene glycol by a cis-diol dehydrogenase.

A large family of multicomponent mononuclear (non-heme) iron oxygenases has been identified. Components of bacterial aromatic-ring dioxygenases constitute two different functional classes: hydroxylase components and electron transfer components. Hydroxylase components are either (αβ)n or (α)n oligomers. Two prosthetic groups, a Rieske-type [Fe2S2] center and a mononuclear iron, are associated with the α-subunit in the (αβ)n-type enzymes. Electron transfer components are composed of flavoprotein (NADH:ferredoxin oxidoreductase) and Rieske-type [Fe2S2] ferredoxin. In benzoate and toluate 1,2-dioxygenase systems, a single protein containing reductase and Rieske-type ferredoxin domains transfers the electrons from NADH to the hydroxylase component. In the phthalate 4,5-dioxygenase system, phthalate dioxygenase reductase (PDR) has the same function. PDR is a single protein comprising FMN-binding reductase and plant-type ferredoxin domains. Thus, the electron transfer in ARHD systems can be summarised as:

    NADH
    reductase
    FAD or FMN
    ferredoxin
    [Fe2S2]
    hydroxylase α-subunit [Fe2S2], Fe

Biochemical classification

benzene 1,2-dioxygenase
benzene + NADH + H+ + O2 = cis-cyclohexa-3,5-diene-1,2-diol + NAD+
phthalate 4,5-dioxygenase
phthalate + NADH + H+ + O2 = cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,2-dicarboxylate + NAD+
4-sulfobenzoate 3,4-dioxygenase
4-sulfobenzoate + NADH + H+ + O2 = 3,4-dihydroxybenzoate + sulfite + NAD+
4-chlorophenylacetate 3,4-dioxygenase
4-chlorophenylacetate + NADH + H+ + O2 = 3,4-dihydroxyphenylacetate + chloride + NAD+
benzoate 1,2-dioxygenase
benzoate + NADH + H+ + O2 = 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate + NAD+
toluene dioxygenase
toluene + NADH + H+ + O2 = (1S,2R)-3-methylcyclohexa-3,5-diene-1,2-diol + NAD+
naphthalene 1,2-dioxygenase
naphthalene + NADH + H+ + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
terephthalate 1,2-dioxygenase
terephthalate + NADH + H+ + O2 = (1R,6S)-dihydroxycyclohexa-2,4-diene-1,4-dicarboxylate + NAD+
biphenyl 2,3-dioxygenase
biphenyl + NADH + H+ + O2 = (1S,2R)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+

Structure

The crystal structure of the hydroxylase component of naphthalene 1,2-dioxygenase from Pseudomonas has been determined. The protein is an (αβ)3 hexamer. The β-subunit belongs to the α+β class. It has no prosthetic groups and its role in catalysis is unknown. The α-subunit can be divided into two domains: a Rieske domain that contains the [Fe2S2] center and the catalytic domain that contains the active site mononuclear iron. The Rieske domain (residues 38-158) consists of four β-sheets. The overall fold is very similar to that of the soluble fragment of the Rieske protein from bovine heart mitochondrial cytochrome bc1 complex. In the [Fe2S2] center, Fe1 is coordinated by two cysteine residues (Cys-81 and Cys-101) while Fe2 is coordinated by Nδ atoms of two histidine residues (His-83 and His-104). The catalytic domain belongs to the α+β class and is dominated by a nine-stranded antiparallel β-sheet. The iron of the active site is located at the bottom of a narrow channel, approximately 15 Å from the protein surface. The mononuclear iron is coordinated by His-208, His-213, Asp-362 (bidentate) and a water molecule. The geometry can be described as a distorted octahedral with one ligand missing. The structure of the hexamer suggests cooperativity between adjacent α-subunits, where electrons from the [Fe2S2] center in one α-subunit (A) are transferred to the mononuclear iron in the adjacent α-subunit (B) through AspB-205, which is hydrogen-bonded to HisA-104 of the Rieske center and HisB-208 of the active site.

References

  • Harayama, S., Kok, M. and Neidle, E.L. (1992). "Functional and evolutionary relationships among diverse oxygenases". Annu. Rev. Microbiol. 46 565–601.
  • Butler, C.S. and Mason, J.R. (1997). "Structure-function analysis of the bacterial aromatic ring-hydroxylating dioxygenases". Adv. Microb. Physiol. 38 47–84.
  • Jiang, H., Parales, R.E., Lynch, N.A. and Gibson, D.T. (1996). "Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: Potential mononuclear non-heme iron coordination sites". J. Bacteriol. 178 3133–3139.
  • Kauppi, B., Lee, K., Carredano, E., Parales, R.E., Gibson, D.T., Eklund, H. and Ramaswamy, S. (1998). "Structure of an aromatic-ring-hydroxylating dioxygenase – naphthalene 1,2-dioxygenase". Structure 6 571–586.

External links

  • - structure of napthalene 1,2-dioxygenase from Pseudomonas putida
  • - structure of biphenyl 2,3-dioxygenase from Rhodococcus sp. strain RHA1
  • - InterPro entry for Bacterial ring hydroxylating dioxygenase, alpha subunit
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