John D. Lipscomb

Versatility of biological non-heme Fe(II) centers in oxygen activation reactions

Oxidase and oxygenase enzymes allow the use of relatively unreactive O2 in biochemical reactions. Many of the mechanistic strategies used in nature for this key reaction are represented within the 2-histidine-1-carboxylate facial triad family of non-heme Fe(II)-containing enzymes. The open face of the metal coordination sphere opposite the three endogenous ligands participates directly in the reaction chemistry. Here, data from several studies are presented showing that reductive O2 activation within this family is initiated by substrate (and in some cases cosubstrate or cofactor) binding, which then allows coordination of O2 to the metal. From this starting point, the O2 activation process and the reactions with substrates diverge broadly. The reactive species formed in these reactions have been proposed to encompass four oxidation states of iron and all forms of reduced O2 as well as several of the reactive oxygen species that derive from O-O bond cleavage.

Protocatechuate 3,4-dioxygenase: Inhibitor studies and mechanistic implications

Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) from Pseudomonas aeruginosa catalyzes the cleavage of 3,4-dihydroxybenzoate (protocatechuate) into beta-carboxy-cis,cis-muconate. The inhibition constants, Ki, of a series of substrate analogues were measured in order to assess the relative importance of the various functional groups on the substrate. Though important for binding, the carboxylate group is not essential for activity. Compounds with para hydroxy groups are better inhibitors than their meta isomers. Our studies of the enzyme-inhibitor complexes indicate that the 4-OH group of the substrate binds to the active-site iron. Taken together, Mössbauer, EPR, and kinetic data suggest a mechanism where substrate reaction with oxygen is preceded by metal activation of substrate.

Mechanism of extradiol aromatic ring-cleaving dioxygenases

The extradiol aromatic ring-cleaving dioxygenases activate molecular oxygen by binding both O(2) and the catecholic substrate to a reduced active site metal, generally Fe(II). Progress has been made in understanding the mechanism of this reaction through the combined use of kinetic, computational, biomimetic, structural, and diagnostic chemical approaches. It appears that O(2) is activated by accepting an electron transferred from the substrate through the metal, thereby simultaneously activating oxygen and substrate for reaction with each other.

Trapping and spectroscopic characterization of an FeIII-superoxo intermediate from a nonheme mononuclear iron-containing enzyme

intermediates are well known in heme enzymes, but none have been characterized in the nonheme mononuclear FeII enzyme family. Many steps in the O2 activation and reaction cycle of FeII-containing homoprotocatechuate 2,3-dioxygenase are made detectable by using the alternative substrate 4-nitrocatechol (4NC) and mutation of the active site His200 to Asn (H200N). Here, the first intermediate (Int-1) observed after adding O2 to the H200N-4NC complex is trapped and characterized using EPR and Mössbauer (MB) spectroscopies. Int-1 is a high-spin (S1 = 5/2) FeIII antiferromagnetically (AF) coupled to an S2 = 1/2 radical (J ≈ 6 cm-1 in ). It exhibits parallel-mode EPR signals at g = 8.17 from the S = 2 multiplet, and g = 8.8 and 11.6 from the S = 3 multiplet. These signals are broadened significantly by hyperfine interactions (A17O ≈ 180 MHz). Thus, Int-1 is an AF-coupled species. The experimental observations are supported by density functional theory calculations that show nearly complete transfer of spin density to the bound O2. Int-1 decays to form a second intermediate (Int-2). MB spectra show that it is also an AF-coupled FeIII-radical complex. Int-2 exhibits an EPR signal at g = 8.05 arising from an S = 2 state. The signal is only slightly broadened by (< 3% spin delocalization), suggesting that Int-2 is a peroxo-FeIII-4NC semiquinone radical species. Our results demonstrate facile electron transfer between FeII, O2, and the organic ligand, thereby supporting the proposed wild-type enzyme mechanism.

Swapping metals in Fe- and Mn-dependent dioxygenases: Evidence for oxygen activation without a change in metal redox state

Biological O2 activation often occurs after binding to a reduced metal [e.g., M(II)] in an enzyme active site. Subsequent M(II)-to-O2 electron transfer results in a reactive M(III)-superoxo species. For the extradiol aromatic ring-cleaving dioxygenases, we have proposed a different model where an electron is transferred from substrate to O2 via the M(II) center to which they are both bound, thereby obviating the need for an integral change in metal redox state. This model is tested by using homoprotocatechuate 2,3-dioxygenases from Brevibacterium fuscum (Fe-HPCD) and Arthrobacter globiformis (Mn-MndD) that share high sequence identity and very similar structures. Despite these similarities, Fe-HPCD binds Fe(II) whereas Mn-MndD incorporates Mn(II). Methods are described to incorporate the nonphysiological metal into each enzyme (Mn-HPCD and Fe-MndD). The x-ray crystal structure of Mn-HPCD at 1.7 Å is found to be indistinguishable from that of Fe-HPCD, while EPR studies show that the Mn(II) sites of Mn-MndD and Mn-HPCD, and the Fe(II) sites of the NO complexes of Fe-HPCD and Fe-MndD, are very similar. The uniform metal site structures of these enzymes suggest that extradiol dioxygenases cannot differentially compensate for the 0.7-V gap in the redox potentials of free iron and manganese. Nonetheless, all four enzymes exhibit nearly the same KM and Vmax values. These enzymes constitute an unusual pair of metallo-oxygenases that remain fully active after a metal swap, implicating a different way by which metals are used to promote oxygen activation without an integral change in metal redox state.

Swapping metals in Fe- and Mn-dependent dioxygenases

Biological O2 activation often occurs after binding to a reduced metal [e.g., M(II)] in an enzyme active site. Subsequent M(II)-to-O2 electron transfer results in a reactive M(III)-superoxo species. For the extradiol aromatic ring-cleaving dioxygenases, we have proposed a different model where an electron is transferred from substrate to O2 via the M(II) center to which they are both bound, thereby obviating the need for an integral change in metal redox state. This model is tested by using homoprotocatechuate 2,3-dioxygenases from Brevibacterium fuscum (Fe-HPCD) and Arthrobacter globiformis (Mn-MndD) that share high sequence identity and very similar structures. Despite these similarities, Fe-HPCD binds Fe(II) whereas Mn-MndD incorporates Mn(II). Methods are described to incorporate the nonphysiological metal into each enzyme (Mn-HPCD and Fe-MndD). The x-ray crystal structure of Mn-HPCD at 1.7 Å is found to be indistinguishable from that of Fe-HPCD, while EPR studies show that the Mn(II) sites of Mn-MndD and Mn-HPCD, and the Fe(II) sites of the NO complexes of Fe-HPCD and Fe-MndD, are very similar. The uniform metal site structures of these enzymes suggest that extradiol dioxygenases cannot differentially compensate for the 0.7-V gap in the redox potentials of free iron and manganese. Nonetheless, all four enzymes exhibit nearly the same KM and Vmax values. These enzymes constitute an unusual pair of metallo-oxygenases that remain fully active after a metal swap, implicating a different way by which metals are used to promote oxygen activation without an integral change in metal redox state.

Substrate activation for O2 reactions by oxidized metal centers in biology

The uncatalyzed reactions of O2 (S = 1) with organic substrates (S = 0) are thermodynamically favorable but kinetically slow because they are spin-forbidden and the one-electron reduction potential of O2 is unfavorable. In nature, many of these important O2 reactions are catalyzed by metalloenzymes. In the case of mononuclear non-heme iron enzymes, either FeII or FeIII can play the catalytic role in these spin-forbidden reactions. Whereas the ferrous enzymes activate O2 directly for reaction, the ferric enzymes activate the substrate for O2 attack. The enzyme–substrate complex of the ferric intradiol dioxygenases exhibits a low-energy catecholate to FeIII charge transfer transition that provides a mechanism by which both the Fe center and the catecholic substrate are activated for the reaction with O2. In this Perspective, we evaluate how the coupling between this experimentally observed charge transfer and the change in geometry and ligand field of the oxidized metal center along the reaction coordinate can overcome the spin-forbidden nature of the O2 reaction.

Mössbauer and EPR spectroscopy on protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa

Protocatechuate 3,4-dioxygenase (EC 1.13.11.3) from Pseudomonas aeruginosa has been investigated by EPR and Mössbauer spectroscopy. Low temperature Mössbauer data on the native enzyme (Fe3+, S = 5/2) yields a hyperfine field Hsat=-525 kG at the nucleus. This observation is inconsistent with earlier suggestions, based on EPR data of a rubredoxin-like ligand environment around the iron, i.e. a tetrahedral sulfur coordination. Likewise, the dithionite-reduced enzyme has Mössbauer parameters unlike those of reduced rubredoxin. We conclude that the iron atoms are in a previously unrecognized environment. The ternary complex of the enzyme with 3,4-dihydroxyphenylpropionate and O2 yields EPR signals at g = 6.7 and g = 5.3; these signals result from an excited state Kramers doublet. The kinetics of the disappearance of these signals parallels product formation and the decay of the ternary complex as observed in the optical spectrum. The Mössbauer and EPR data on the ternary complex establish the iron atoms to be a high-spin ferric state characterized by a large and negative zero-field splitting, D = approximately -2 cm-1.

A ‘blue’ copper oxidase from Nitrosomonas europaea

Abstract A soluble copper-containing protein with p -phenylenediamine oxidase activity was purified from Nitrosomonas europaea by flat-bed isoelectric focusing and chromatography on Sephacryl S-300. The native and subunit molecular weights were 127 500 and 40 100, respectively; the isoelectric point was pH 4.63. The protein had an absorption maximum at 607 nm in the oxidized form with an extinction coefficient of 6.0 cm −1 · mM −1 at pH 7.5. On reduction with dithionite, the absorbance was abolished. The electron paramagnetic resonance spectrum of the protein showed evidence for both Type 1 and Type 2 copper in a 1:1 ratio. The protein catalyzed the aerobic oxidation of p -phenylenediamine, cytochrome c -554, and hydroxylamine oxidoreductase. The enzyme catalyzed the reduction of nitrite with cytochrome c -552 as electron donor. In contrast, p -phenylenediamine, reduced cytochrome c -554, and hydroxylamine oxidoreductase were not active as electron donors for nitrite reduction.

HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM BREVIBACTERIUM FUSCUM : A DIOXYGENASE WITH CATALASE ACTIVITY

Homoprotocatechuate 2,3-dioxygenase (2,3-HPCD) cleaves the aromatic ring of its substrate with insertion of both atoms of oxygen from O2 to form α-hydroxy--carboxymethyl cis-muconic semialdehyde. The enzyme has been purified from the Gram-positive bacterium Brevibacterium fuscum and characterized. The enzyme appears to have a range of quaternary structures with predominant components of α4 and α6 (α subunit Mr = 42500 ± 1500) and binds 1 Fe(II)/subunit. Although the substrate K values are similar to those of other Fe(II) ring cleaving dioxygenases, the turnover number is lower by 90-97%, and the enzyme exhibits much higher stability to metal chelators and H2O2. The stability to H2O2 is shown to derive from an endogenous catalase activity of 2,3-HPCD (stoichiometry: 2 H2O2 2 H2O + O2) that is novel for dioxygenases. H2O2 is a mixed-type inhibitor of the dioxygenase activity, suggesting that dioxygenase and catalase activities are both catalyzed by the enzyme, but at distinguishable sites. In contrast, catecholic substrates, including homoprotocatechuate and p-nitrocatechol, are nonessential activators of the catalase activity. The plot of 1/v of catalase activity versus 1/[H2O2] is parabolic in the absence of catecholic substrates and linear in their presence, indicating that these reactions proceed by different mechanisms. A mechanism for catalase activity is proposed in which 2 H2O2 molecules bind simultaneously to the iron to account for the observed parabolic kinetic plot. Electron transfer between the peroxides mediated by the iron would yield 2 H2O and O2. Catecholic substrates are proposed to modify this reaction by excluding one H2O2 from the Fe(II), thereby causing the kinetic plots to appear linear. Electron donation by the catecholic substrates would facilitate O-O bond cleavage of H2O2, but outer sphere electron transfer from a second H2O2 in another step would be necessary to complete the reaction. p-Nitrocatechol is shown to bind differently to 2,3-HPCD than to other Fe(II) ring cleavage dioxygenases. Possible explanations for this observation are considered in the context of the proposed catalase and normal dioxygenase mechanisms which may also have bearing on the unique catalase activity and low dioxygenase turnover number of the enzyme.