Fe III -O 2 •− intermediates are well known in heme enzymes, but none have been characterized in the nonheme mononuclear Fe II enzyme family. Many steps in the O 2 activation and reaction cycle of Fe II -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 O 2 to the H200N-4NC complex is trapped and characterized using EPR and Möss-bauer (MB) spectroscopies. Int-1 is a high-spin ( (1)(2)(3)(4)(5)(6)(7)(8). Internal electron transfer to form an Fe III -superoxo species converts the kinetically inert triplet ground state of O 2 to a doublet that can participate in the many types of chemistry characteristic of this mechanistically diverse group of enzymes. The same strategy is usually employed by heme-containing oxygenases and oxidases, leading in some cases to comparatively stable Fe III -superoxo intermediates that have been structurally and spectroscopically characterized (9-12). Instability of the putative superoxo intermediate in all mononuclear nonheme iron-containing enzymes has prevented similar characterization, although a superoxide level species has been reported for the dinuclear iron site of myo-inositol oxygenase (13).In recent studies of the nonheme Fe II -containing homoprotocatechuate 2,3-dioxygenase (2,3-HPCD), we have shown that three intermediates of the catalytic cycle can be trapped in one crystal for structural analysis (14). One of these intermediates has been proposed to be an Fe II -superoxo species based on the long Fe-O bond distances and an unexpected lack of planarity of the aromatic ring of the alternative substrate 4-nitrocatechol (4NC), which chelates the iron in ligand sites adjacent to that of the O 2 . In accord with the mechanism postulated for this enzyme class as illustrated in Scheme 1 (1, 8, 15-21), we have proposed that net electron transfer from 4NC through the Fe II to O 2 forms adjacent substrate and oxygen radicals (Scheme 1B). Recombination of the radicals would begin the ring cleavage and oxygen insertion reactions of this enzyme that eventually yield a muconic semialdehyde adduct as the product. A localized radical on the 4NC semiquinone at the incipient position of oxygen attack would account for the lack of ring planarity. Although this is the only structurally characterized nonheme Fe-superoxo species, the iron oxidation state differs from all of the other postulated Fe-superoxo intermediates.The mechanism that emerges from the structural and kinetic studies does not require a change in metal oxidation state to form a reactive intermediate (22). However, our studies of 2,3-HPCD in which Fe II is replaced with Mn II suggest that transient formaScheme 1. Proposed mechanism for extradiol dioxygenases. In the case of 2,3-HPCD, R is −CH 2 COO − and B is His200. When R is −NO 2 and His200 is changed to Asn, the reaction stalls before reaching intermediate C. Peroxide is slowly released a...

Substrates homoprotocatechuate (HPCA) and O2 bind to the FeII of Homoprotocatechuate 2,3-dioxygenase (FeHPCD) in adjacent coordination sites. Transfer of an electron(s) from HPCA to O2 via the iron is proposed to activate the substrates for reaction with each other to initiate aromatic ring cleavage. Here, rapid-freeze-quench methods are used to trap and spectroscopically characterize intermediates in the reactions of the HPCA complexes of FeHPCD and the variant His200Asn (FeHPCD-HPCA and H200N-HPCA) with O2. A blue intermediate forms within 20 ms after mixing O2 with H200N-HPCA (H200NInt1HPCA). Parallel mode EPR and Mössbauer spectroscopies show that this intermediate contains high-spin FeIII (S=5/2) antiferromagnetically coupled to a radical (SR=1/2) to yield an S=2 state. Together, optical and Mössbauer spectra of the intermediate support assignment of the radical as an HPCA semiquinone, implying that oxygen is bound as a (hydro)peroxo ligand. H200NInt1HPCA decays over the next 2 s, possibly through an FeII intermediate (H200NInt2HPCA), to yield product and the resting FeII enzyme. Reaction of FeHPCD-HPCA with O2 results in rapid formation of a colorless FeII intermediate (FeHPCDInt1HPCA). This species decays within 1 s to yield the product and the resting enzyme. The absence of a chromophore from a semiquinone or evidence for a spin-coupled species in FeHPCDInt1HPCA suggests it is an intermediate occurring after O2 activation and attack. The similar Mössbauer parameters for FeHPCDInt1HPCA and H200NInt2HPCA suggest these are similar intermediates. The results show that electron transfer from the substrate to the O2 via the iron does occur leading to aromatic ring cleavage.

Stilbenes are diphenyl ethene compounds produced naturally in a wide variety of plant species and some bacteria. Stilbenes are also derived from lignin during kraft pulping. Stilbene cleavage oxygenases (SCOs) cleave the central double bond of stilbenes, forming two phenolic aldehydes. Here, we report the structure of an SCO. The X-ray structure of NOV1 from Novosphingobium aromaticivorans was determined in complex with its substrate resveratrol (1.89 Å), its product vanillin (1.75 Å), and without any bound ligand (1.61 Å). The enzyme is a seven-bladed β-propeller with an iron cofactor coordinated by four histidines. In all three structures, dioxygen is observed bound to the iron in a side-on fashion. These structures, along with EPR analysis, allow us to propose a mechanism in which a ferric-superoxide reacts with substrate activated by deprotonation of a phenol group at position 4 of the substrate, which allows movement of electron density toward the central double bond and thus facilitates reaction with the ferric superoxide electrophile. Correspondingly, NOV1 cleaves a wide range of other stilbene-like compounds with a 4′-OH group, offering potential in processing some solubilized fragments of lignin into monomer aromatic compounds.tilbenes are diphenyl ethene compounds that are produced naturally in a wide variety of plant species and some bacteria. One stilbene derivative of note is resveratrol, which is a plant phytoalexin abundant in grapes and peanuts. Studies have demonstrated numerous health benefits related to the consumption of resveratrol, which is correlated with reduced cardiovascular disease and cancer (1). Lignostilbene α,β-dioxygenase (LSD, EC 1.13.11.43), originally observed in Sphingomonas paucimobilis, was the first enzyme shown to cleave the central double bond of stilbenes, forming two phenolic aldehydes (2, 3). Subsequently, NOV1 and NOV2 (4) from Novosphingobium aromaticivorans, Rco1 (5) from Ustilago maydis, and CAO-1 (6) from Neurospora crassa were also shown to be stilbene cleaving oxygenases (SCOs). SCOs are related to carotenoid cleavage oxygenases (CCOs), which are enzymes that oxidatively cleave β-carotene or apocarotenoids. Carotenoids are a diverse class of molecules that play important roles in photosynthesis, immune function, and light perception in the eye. CCOs have been studied in great detail, including several crystal structures (7-9).Here, we present the X-ray structure of an SCO, NOV1 from N. aromaticivorans (NOV1). The structure was determined in complex with a representative substrate (resveratrol), a representative product (vanillin), and without ligand bound. We have also observed the ternary complex with oxygen and substrate or product bound, which has not been previously detected in a crystal structure of any CCO-related enzyme. Despite being related to CCOs, this structure of NOV1 shows several key differences that are indicative of their disparate substrate specificities. Moreover, the observed placement of Fe, O 2 , and the phenolic substrate resveratrol in th...

Homoprotocatechuate (HPCA; 3,4-dihydroxyphenylacetate or 4-carboxymethyl catechol) and O2 bind in adjacent ligand sites of the active site FeII of Homoprotocatechuate 2,3-Dioxygenase (FeHPCD). We have proposed that electron transfer from the chelated aromatic substrate through the FeII to O2 gives both substrates radical character. This would promote reaction between the substrates to form an alkylperoxo intermediate as the first step in aromatic ring cleavage. Several active site amino acids are thought to promote these reactions through acid/base chemistry, hydrogen bonding, and electrostatic interactions. Here the role of Tyr257 is explored by using the Tyr257Phe (Y257F) variant, which decreases kcat by about 75%. The crystal structure of the FeHPCD-HPCA complex has shown that Tyr257 hydrogen bonds to the deprotonated C2-hydroxyl of HPCA. Stopped-flow studies show that at least two reaction intermediates, termed Y257FInt1HPCA and Y257FInt2HPCA, accumulate during the Y257F-HPCA + O2 reaction prior to formation of the ring-cleaved product. Y257FInt1HPCA is colorless and is formed as O2 binds reversibly to the HPCA-enzyme complex. Y257FInt2HPCA forms spontaneously from Y257FInt1HPCA and displays a chromophore at 425 nm (ε425 = 10,500 M-1 cm−1). Mössbauer spectra of the intermediates trapped by rapid freeze quench show that both intermediates contain FeII. The lack of a chromophore characteristic of a quinone or semiquinone form of HPCA, the presence of FeII, and the low O2 affinity suggests that Y257FInt1HPCA is an HPCA-FeII-O2 complex with little electron delocalization onto the O2. In contrast, the intense spectrum of Y257FInt2HPCA suggests the intermediate is most likely an HPCA quinone-FeII-(hydro)peroxo species. Steady-state and transient kinetic analyses show that steps of the catalytic cycle are slowed by as much as 100-fold by the mutation. These effects can be rationalized by a failure of Y257F to facilitate the observed distortion of the bound HPCA that is proposed to promote transfer of one electron to O2.

The extradiol-cleaving dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) binds substrate homoprotocatechuate (HPCA) and O2 sequentially in adjacent ligand sites of the active site FeII. Kinetic and spectroscopic studies of HPCD have elucidated catalytic roles of several active site residues, including the crucial acid base chemistry of His200. In the present study, reaction of the His200Cys (H200C) variant with native substrate HPCA resulted in a decrease in both kcat and the rate constants for the activation steps following O2 binding by > 400 fold. The reaction proceeds to form the correct extradiol product. This slow reaction allowed a long-lived (t1/2 = 1.5 min) intermediate, H200C-HPCAInt1 (Int1), to be trapped. Mössbauer and parallel mode electron paramagnetic resonance (EPR) studies show that Int1 contains an S1 = 5/2 FeIII center coupled to an SR = 1/2 radical to give a ground state with total spin S = 2 (J > 40 cm−1) in scriptHexch=JtrueS^1⋅trueS^normalR. Density functional theory (DFT) property calculations for structural models Int1 is a (HPCA semiquinone•)FeIII(OOH) complex, in which OOH is protonated at the distal O and the substrate hydroxyls are deprotonated. By combining Mössbauer and EPR data of Int1 with DFT calculations, the orientations of the principal axes of the 57Fe electric field gradient and the zero-field splitting (ZFS) tensors (D = 1.6 cm−1, E/D = 0.05) were determined. This information was used to predict hyperfine splittings from bound 17OOH. DFT reactivity analysis suggests that Int1 can evolve from a ferromagnetically coupled FeIII-superoxo precursor by an inner-sphere proton-coupled-electron-transfer process. Our spectroscopic and DFT results suggest that a ferric hydroperoxo species is capable of extradiol catalysis.

The extradiol dioxygenases are a large subclass of mononuclear non-heme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O2. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O2-4NC species and a Fe-O2-4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as FeIII-superoxo-catecholate and FeIII-peroxysemiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of non-heme Fe-O2 intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on FeIII-superoxocatecholate and an end-on FeIII-hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a FeIII-hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of FeIII-superoxo and FeIII-hydroperoxo intermediates in non-heme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.

Background Immunosuppressant therapeutic drug monitoring (TDM) usually requires outpatient travel to hospitals or phlebotomy sites for venous blood collection; however Mitra® Microsampling Device (MSD) sampling could allow self-collection and shipping of samples to a laboratory for analysis. This study examined the feasibility of using volumetric microsampling by MSD for TDM of tacrolimus (TaC) and cyclosporin A (CsA) in transplant patients, along with their feedback on the process. Methods MSD was used to collect TaC and CsA from venous (VB) or capillary (CB) blood. The MSDs were rehydrated, extracted, and analyzed using on-line solid phase extraction coupled to tandem mass spectrometry (SPE-MS/MS). We report an abbreviated method validation of the MSD including: accuracy, precision, linearity, carry-over, and stability using residual venous whole blood (VB) samples. Subsequent clinical validation compared serially collected MSD + CB against VB (200 µL) from transplant patients. Results Accuracy comparing VB vs. MSD+VB showed high clinical concordance (TaC = 89% and CsA = 98%). Inter- and intra-precision was ≤11.5 %CV for TaC and CsA. Samples were stable for up to 7 days at room temperature with an average difference of <10%. Clinical validation with MSD+CB correlated well with VB for CsA (slope = 0.95, r2 = 0.88, n = 47) and TaC (slope = 0.98, r2 = 0.82, n = 49). CB vs. VB gave concordance of 94% for CsA and 79% for TaC. A satisfaction survey showed 82% of patients preferred having the capillary collection option. Conclusion Transplant patients favored having the ability to collect capillary samples at home for TaC/CsA monitoring. Our results demonstrate good concordance between MSD+CB and VB for TaC and CsA TDM, but additional studies are warranted.

In PNAS (1) Kiser has expressed some skepticism about the identity of the active-site dioxygen molecule and suggests that the density is better modeled with two water molecules at partial occupancy. In response, we have performed an extended analysis with the following results. There are currently 321 entries for proteins containing dioxygen (PDB OXY) in the Protein Data Bank (PDB). As might be expected, the electron density ranges from highly symmetric to highly irregular. For example, naphthalene 1,2-dioxygenase [PDB ID code 1O7N (2)], cited by Kiser as a comparable enzyme, has a dioxygen bound in a sideon manner to an iron in almost exactly the same orientation as the NOV1 structures with and without substrate (3). Like NOV1, the density surrounding the dioxygen is not completely symmetric, and there are many more examples in the PDB. Oxygen atoms from a dioxygen species that are in identical chemical environments have more regular density and similar B-factors, although the opposite is also true. In apo-NOV1 (PDB ID code 5J53), a solvent molecule is 2.4 Å from the oxygen atom that is most closely bound to the iron, and it may perturb the oxygen's position. This may also address Kiser's second critique, which is that the two oxygens have different B-factors and the oxygen closer to the iron has the high B-factor. Naphthalene 1,2-dioxygenase (PDB ID code 1O7N) also has a higher B-factor for the oxygen bound more closely to the iron, and a survey of OXY PDB entries shows that the B-factors are often quite different. Finally, Kiser reports that refinement of individual oxygen atoms or an unrestrained dioxygen results in O-O distances of ∼1.8 Å, which is longer than the expected 1.2 Å. However, as has been pointed out by others, unrestrained refinement should only be used for ultra-high-resolution structures with observations to parameters ratios of 10 or greater (4). Below that ratio, the uncertainty will be very large, and the results may be meaningless. To demonstrate this, we refined a number of related dioxygen-bound structures this way (Table 1). Naphthalene 1,2-dioxygenase (PDB ID code 1O7N) (2) and homogentisate 1,2-dioxygenase (PDB ID code 3ZDS) (5) both bind dioxygen similarly to NOV1. They refine to distances that are much higher (∼1.8 Å) or lower (∼0.9 Å) than dioxygen. When we performed the same refinement on apo-NOV1 (PDB ID code 5J53), we did not obtain the distances reported by Kiser. They were only slightly larger than standard dioxygen (Table 1), and we note that when the occupancy of the dioxygen in apo-NOV1 (PDB ID code 5J53) is lowered the distances converge on 1.2 Å (Table 1) and the B-factors also decrease. The occupancies of the dioxygen were refined in both NOV1 structures, but at the data resolutions involved B-factors and occupancies are highly correlated (4). Therefore, it is possible that the dioxygen could be modeled with an occupancy slightly lower than the refined value of 0.9. In summary, our original paper and the analyses presented here show that Kiser's statements in no way pre...