Reaction mechanisms of non-heme diiron hydroxylases characterized in whole cells

Whole cells expressing the non-heme diiron hydroxylases AlkB and toluene 4-monooxygenase (T4MO) were used to probe enzyme reaction mechanisms. AlkB catalyzes the hydroxylation of the radical clock substrates bicyclo[4.1.0]heptane (norcarane), spirooctane and 1,1-diethylcyclopropane, and does not catalyze the hydroxylation of the radical clocks 1,1-dimethylcyclopropane or 1,1,2,2-tetramethylcyclopropane. The hydroxylation of norcarane yields a distribution of products consistent with an "oxygen-rebound" mechanism for the enzyme in both the wild type Pseudomonas putida GPo1 and AlkB from P. putida GPo1 expressed in Escherichia coli. Evidence for the presence of a substrate-based radical during the reaction mechanism is clear. With norcarane, the lifetime of that radical varies with experimental conditions. Experiments with higher substrate concentrations yield a shorter radical lifetime (approximately 1 ns), while experiments with lower substrate concentrations yield a longer radical lifetime (approximately 19 ns). Consistent results were obtained using either wild type or AlkB-equipped host organisms using either "resting cell" or "growing cell" approaches. T4MO expressed in E. coli also catalyzes the hydroxylation of norcarane with a radical lifetime of approximately 0.07 ns. No radical lifetime dependence on substrate concentration was seen. Results from experiments with diethylcyclopropane, spirooctane, dimethylcyclopropane, and diethylcyclopropane are consistent with a restricted active site for AlkB.

Estimation of the age of human bloodstains by electron paramagnetic resonance spectroscopy: long-term controlled experiment on the effects of environmental factors

In this study, we examined the efficacy and limitations of electron paramagnetic resonance (EPR) for estimating the age of human bloodstains. At 77K, human bloodstains give four striking EPR signals in the g=6.2 (g6), 4.3 (g4), 2.27 (H) and 2.005 (R) regions due to ferric high-spin, ferric non-heme, ferric low-spin and free radical species, respectively. We found that plotting double logarithms of the EPR intensity ratio of H/g4 versus days past bleeding gave a linear correlation up to 432 days with an error range within 25% of the actual number of days under controlled conditions. However, environmental factors such as differences of absorbent, light exposure and fluctuations of storage temperature affected the changes of these EPR-active compounds, which result in misestimation of the time since bleeding occurred. Therefore, one should take such factors into account in estimating the period since bleeding by this method.

Genetic variation of basal iron status, ferritin and iron regulatory protein in mice: potential for modulation of oxidative stress

Toxic and carcinogenic free radical processes induced by drugs and other chemicals are probably modulated by the participation of available iron. To see whether endogenous iron was genetically variable in normal mice, the common strains C57BL/10ScSn, C57BL/6J, BALB/c, DBA/2, and SWR were examined for major differences in their hepatic non-heme iron contents. Levels in SWR mice were 3- to 5-fold higher than in the two C57BL strains, with intermediate levels in DBA/2 and BALB/c mice. Concentrations in kidney, lung, and especially spleen of SWR mice were also greater than those in C57BL mice. Non-denaturing PAGE of hepatic ferritin from all strains showed a major holoferritin band at approximately 600 kDa, with SWR mice having > 3-fold higher levels than C57BL strains. SDS PAGE showed a band of 22 kDa, mainly representing L-ferritin subunits. A trace of a subunit at 18 kDa was also detected in ferritin from SWR mice. The 18 kDa subunit and a 500 kDa holoferritin from which it originates were observed in all strains after parenteral iron overload, and there was no major variation in ferritin patterns. Although iron uptake studies showed no evidence for differential duodenal absorption between strains to explain the variation in basal iron levels, acquisition of absorbed iron by the liver was significantly higher in SWR mice than C57BL/6J. As with iron and ferritin contents, total iron regulatory protein (IRP-1) binding capacity for mRNA iron responsive element (IRE) and actual IRE/IRP binding in the liver were significantly greater in SWR than C57BL/6J mice. Cytosolic aconitase activity, representing unbound IRP-1, tended to be lower in the former strain. SWR mice were more susceptible than C57BL/10ScSn mice to the toxic action of diquat, which is thought to involve iron catalysis. If extrapolated to humans, the findings could suggest that some people might have the propensity for greater basal hepatic iron stores than others, which might make them more susceptible to iron-catalysed toxicity caused by oxidants.

Spin-lattice relaxation of the pheophytin, Pheo-, radical of photosystem II

The spin-lattice relaxation times (T1) of the pheophytin anion radical, Pheo-, of the PSII reaction center, were measured between 5 and 80 K by electron spin-echo spectroscopy. The Pheo- was studied in Mn-depleted PSII reaction centers in which the primary quinone, QA, was doubly reduced. The selective conversion of the non-heme Fe2+ into its low-spin (S = O) state, in CN-treated PSII, allowed the measurement of the intrinsic T1 of the Pheo- radical. The temperature dependence of the intrinsic (T1)-1 was found to be approximately T1.3 +/- 0.1. In Mn-depleted PSII membranes the high-spin (S = 2) non-heme iron, enhances the spin-lattice relaxation of Pheo-. By analyzing the data with a dipolar model, the dipolar interaction (k1d) between the Pheo and the Fe2+ (S = 2) is estimated over the temperature range 5-80 K. Comparison with the dipolar coupling between the iron and the tyrosine, YD+, shows that the Pheo is much closer to the iron than the YD+ in the PSII reaction center. By scaling the reported Fe(2+)-YD+ distance by the ratio [k1dPheo-]/[k1dYD+], we estimate the Fe(2+)-Pheo- distance in PSII to be 20 +/- 4.2 A. This distance is close to the Fe(2+)-BPheo- distance in the bacterial reaction center, and this result provides further evidence that the acceptor sides of the reaction centers in PSII and bacteria are homologous.

Bicarbonate binding to the non-heme iron of photosystem II investigated by Fourier transform infrared difference spectroscopy and 13C-labeled bicarbonate

The binding site of the non-heme iron of photosystem II (PS II) is investigated by light-induced Fourier tranform infrared (FTIR) difference spectroscopy on Tris-washed membranes. The non-heme iron is oxidized (Fe3+) in the dark with ferricyanide and reduced (Fe2+) after light-induced charge separation by electron transfer from the semiquinone anion QA-. EPR experiments and IR modes of ferri- and ferrocyanide show that the electron donor side of PS II is reduced in less than 2 s after a flash and that ferricyanide reoxidizes the non-heme iron with a half-time of approximately 20 s. Recording FTIR spectra before and 2 s after flash illumination thus results in the Fe2+/Fe3+ difference spectrum. This spectrum shows band shifts and intensity changes of IR modes from ligands and neighboring residues of the non-heme iron. The IR modes of bicarbonate are revealed by comparison of Fe2+/Fe3+ spectra obtained on PS II membranes with 12C or 13C isotope labeled bicarbonate in H2O and in 2H2O. The nu as(CO) and nu s(CO) modes of bicarbonate in the Fe2+ state are assigned at 1530 +/- 10 and 1338 cm-1, respectively. The low frequency of the nu as(CO) mode is taken as experimental evidence that bicarbonate is a ligand of the non-heme iron. Furthermore, the small frequency difference (192 cm-1) between the nu as(CO) and nu s(CO) modes as compared to even hydrogen-bonded ionic bicarbonate strongly indicates that bicarbonate is a bidentate ligand of the non-heme iron in PS II. Upon iron oxidation, the bicarbonate modes are largely affected. The nu s(CO) mode is assigned at 1228 cm-1, while the nu as(CO) mode is tentatively assigned at 1658 +/- 20 cm-1. The strong up- and downshifts of the nu as and nu s(CO) modes of bicarbonate upon iron oxidation results in a frequency difference of 430 +/- 20 cm-1 that is not only explained by the increased charge on the iron but indicates that bicarbonate is a monodentate ligand of the oxidized iron. The sensitivity of the nu s(CO) mode of bicarbonate to 1H/2H exchange in both the Fe2+ and Fe3+ states and the presence in the Fe2+ state of a delta (COH) mode at 1258 cm-1 confirm that bicarbonate and not carbonate is the iron ligand and further exhibits hydrogen bond(s) with the protein. The 13C isotope-sensitive modes of bicarbonate are not affected by 15N labeling of the PS II membranes. 15N sensitive signals at 1111/1102 and 1094 cm-1 are assigned to side chain modes from histidine ligands of the iron. The latter signal is proposed to account for a histidine ligand that deprotonates upon iron oxidation. The involvement of protein peptide groups and side chains in the hydrogen-bond network around the iron is also discussed.

Mechanism of metal-independent hydroxylation by Chromobacterium violaceum phenylalanine hydroxylase

Phenylalanine hydroxylase converts phenylalanine to tyrosine utilizing a tetrahydrobiopterin cofactor. Several key mechanistic questions have yet to be resolved, specifically the identity of the hydroxylating species and the role of the non-heme iron which is present in all of the mammalian PAHs. Recently, we have demonstrated that a bacterial PAH from Chromobacterium violaceum does not require any redox active metal for activity [Carr, R. T., & Benkovic, S. J. (1993) Biochemistry 32, 14132-14138]. To identify the function of iron in the mammalian PAH's, we have undertaken a series of experiments to compare the mechanisms of this metal-independent PAH with the iron-dependent PAH from rat liver. Using [4-2H]phenylalanine as a substrate gave a kinetic isotope effect on hydroxylation of unity for CVPAH which is in agreement with previous values reported for RLPAH. The [4-2H]phenylalanine underwent an NIH shift upon hydroxylation by CVPAH. The extent of deuterium retention at the 3-position of the tyrosine product was identical within experimental error for both RLPAH and CVPAH using [4-2H]phenylalanine and [2,3,5,6-2H]phenylalanine as substrates. This suggests that PAH from either source probably does not directly mediate the NIH shift mechanism. No uncoupled pterin turnover was observed for CVPAH with either L-tyrosine or p-chloro-L-phenylalanine as substrate or tetrahydropterin as cofactor, each of which causes uncoupled turnover with RLPAH. CVPAH readily accepts 4-methylphenylalanine as a substrate giving 4-(hydroxymethyl)phenylalanine as the major product and 3-methyltyrosine as the only other minor product.(ABSTRACT TRUNCATED AT 250 WORDS)

Structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15 A resolution

Protocatechuate 3,4-dioxygenase catalyzes the aromatic ring cleavage of 3,4-dihydroxybenzoate by incorporating both atoms of molecular oxygen to yield beta-carboxy-cis,cis-muconate. The structure of this metalloenzyme from Pseudomonas aeruginosa (now reclassified as P. putida) has been refined to an R-factor of 0.172 to 2.15 A resolution. The structure is a highly symmetric (alpha beta Fe3+)12 aggregate with a root-mean-square (r.m.s.) difference of 0.18 A among symmetry-related atoms. The tertiary structure of the two polypeptides (alpha and beta) are highly homologous (r.m.s. difference of 1.05 A over 127 C alpha atoms), suggesting that the ancestral enzyme was originally a homodimer with two active sites. Indeed, a non-functional, vestigial active site retains many of the properties of the functional active site but does not bind iron. The coordination geometry of the non-heme iron catalytic cofactor can best be described as trigonal bipyramidal with Tyr447 (147 beta) and His462 (162 beta) serving as axial ligands, and Tyr408 (108 beta), His460 (160 beta) and Wat837 serving as equitorial ligands. The active site environment has a number of basic residues that may promote binding of the acidic substrate. Within the putative active site cavity which is located between alpha and beta chains, five approximately coplanar solvent molecules suggest a position for the planar substrate Trp449 (149 beta), Ile491 (191 beta), defined by Gly14 (14 alpha) and Pro15 (15 alpha). In this position the guanidino group of Arg457 (157 beta) would be buried by the substrate, suggesting a functional role in catalysis.

A blue non-heme iron protein from Desulfovibrio gigas

A novel iron-containing blue protein, named neelaredoxin, was isolated from the sulfate-reducing bacterium Desulfovibrio gigas. It is a monomeric protein with a molecular mass of 15 kDa containing two iron atoms/molecule. The N-terminal sequence of neelaredoxin has similarity to the second domain of desulfoferrodoxin, a protein purified from Desulfovibrio vulgaris Hildenborough. This finding supports the hypothesis that the gene coding for desulfoferrodoxin (rbo) might have arisen from a gene fusion [Brumlik, M. J., Leroy, G., Bruschi, M. & Voordouw, G. (1990) J. Bacteriol. 172, 7289-7292]. The visible spectrum exhibits a single band at 666 nm, responsible for the blue color of the protein, which is completely bleached upon reduction with sodium ascorbate. In the oxidized state the EPR spectrum is complex, exhibiting well-resolved features at g = 7.6, 7.0, 5.9, and 5.8 which are assigned to two high-spin (S = 5/2) mononuclear-iron (III) centers with different rhombic distortions (E/D approximately 0.05 and approximately 0.08). The two iron atoms contribute identically to the visible spectrum as judged from visible redox titrations, from which a reduction potential of +190 mV was determined for both iron sites at pH 7.5. At high pH the visible and the EPR spectra become pH-dependent with a pKa above 9: the 666-nm band shifts to 590 nm and the EPR signals are converted into a signal with gmax approximately 4.7. Neelaredoxin is readily reduced both by H2/hydrogenase/cytochrome c3 and by NADH/NADH-rubredoxin oxidoreductase.

The structure and function of lipoxygenase

Lipoxygenases are non-heme iron enzymes that catalyze the dioxygenation of polyunsaturated fatty acids, yielding hydroperoxides. The first crystal structures have recently been published, revealing an unusual iron site. There have also been substantial developments in the analysis of the kinetics of the reaction, including the observation of uniquely large primary deuterium isotope effects. Exploitation of these results should enable substantial progress in understanding what appears to be a complicated and fascinating chemical mechanism.

Characterization of the gene encoding the iron-sulfur protein subunit of succinate dehydrogenase from Drosophila melanogaster

The iron-sulfur protein (Ip) subunit of succinate dehydrogenase (and complex II of the electron transport chain) is highly conserved in evolution [Gould et al., Proc. Natl. Acad. Sci. USA 86 (1989) 1934-1938]. We have cloned the Drosophila melanogaster Ip-encoding gene (SdhB) by genomic library screening using the human Ip-encoding cDNA as a probe at low stringency. A 2.7-kb fragment containing SdhB has been sequenced and shown to comprise the entire transcribed region and more than 900 bp of promoter region. The gene contains three exons and two small introns of 272 and 56 nt, respectively, and is transcribed into an mRNA of 1205 nt (plus poly(A) tail). The deduced amino-acid (aa) sequence shows strong similarities with Ip peptides from Escherichia coli, yeasts, plants and mammals, with 100% aa identity around the three Cys clusters which form the non-heme iron-sulfur centers. In situ hybridization on polytene chromosomes maps SdhB to band 42D 1-5 on the right arm of the second chromosome next to the centromere. Developmental and tissue-specific Northern blots show a single transcript of 1.3 kb in all tissues. However, its abundance varies during development and in the major body segments of the adult fly. Pupae have very low levels of transcript, in contrast to larvae. It is most abundant in the adult thorax and low in abdominal tissues.

Identification of amino acid residues associated with the [2Fe-2S] cluster of the 25 kDa (NQO2) subunit of the proton-translocating NADH-quinone oxidoreductase of Paracoccus denitrificans

In order to identify the ligand residues of the [2Fe-2S] cluster of the 25 kDa (NQO2) subunit of the proton-translocating NADH-quinone oxidoreductase of Paracoccus denitrificans, we mutated individually all seven cysteine residues (C61, C96, C101, C104, C113, C137, and C141) and one conserved histidine residue (H92) to Ser or Ala and expressed them in E. coli. After purification of the mutated 25 kDa subunits, the effect of mutations on the iron-sulfur cluster were characterized by chemical analyses and UV-visible and EPR spectroscopy. All mutated subunits, especially mutants of conserved cysteines, contained lower amounts of non-heme iron than wild-type. The subunits of three non-conserved cysteine residues (C61, C104, and C113) mutated to Ser and a histidine residue (H92) mutated to Ala exhibited essentially the same spectroscopic properties as those of the wild-type subunit. In contrast, mutation of the four conserved cysteine residues (C96, C101, C137, and C141) to Ser or Ala considerably altered the UV-visible and EPR spectra from the wild-type subunit. These results indicate that the four conserved cysteine residues coordinate the [2Fe-2S] cluster in the P. denitrificans 25 kDa subunit.

F420H2: quinone oxidoreductase from Archaeoglobus fulgidus. Characterization of a membrane-bound multisubunit complex containing FAD and iron-sulfur clusters

Archaeoglobus fulgidus, a hyperthermophilic sulfate-reducing archaeon, was found to contain a membrane-bound F420H2: quinone oxidoreductase complex presumed to be involved in energy conservation during growth on lactate plus sulfate. After solubilization with dodecyl-beta-D-maltoside the complex was purified 32-fold with a yield of 24%. Using both gel filtration and native PAGE, an apparent molecular mass of approximately 270 kDa was determined. SDS/PAGE revealed the presence of at least seven polypeptides with apparent molecular masses 56, 45, 41, 39, 37, 33, and 32 kDa. The purified complex contained 1.6 mol FAD, 9 mol non-heme iron and 7 mol acid-labile sulfur/mol complex. It did not contain cytochromes, which were, however, present in the membrane fraction of A. fulgidus (3 nmol/mg membrane protein). The purified F420H2: quinone oxidoreductase complex catalyzed the reduction of 2,3-dimethyl-1,4-naphthoquinone (apparent Km 190 microM) with reduced coenzyme F420 (apparent Km 50 microM) exhibiting a specific activity of 500 U/mg (apparent Vmax) at pH 8.0 (pH optimum) and 65 degrees C (temperature optimum). 2-Methyl-1,4-naphthoquinone (menadione), 2-hydroxy-1,4-naphthoquinone, 1,4-naphthoquinone, 2,3-dimethoxy-5-methyl-1,4- benzoquinone, and 2,3-dimethoxy-5-methyl-6-decyl-1,4-benzoquinone (decyl-ubiquinone) were also reduced with F420H2, albeit with lower rates. The physiological electron acceptor of the F420H2: quinone oxidoreductase complex is most likely the menaquinone found in the membrane fraction of A. fulgidus.

Spectroscopic properties of desulfoferrodoxin from Desulfovibrio desulfuricans (ATCC 27774)

Desulfoferrodoxin, a non-heme iron protein, was purified previously from extracts of Desulfovibrio desulfuricans (ATCC 27774) (Moura, I., Tavares, P., Moura, J. J. G., Ravi, N., Huynh, B. H., Liu, M.-Y., and LeGall, J. (1990) J. Biol. Chem. 265, 21596-21602). The as-isolated protein displays a pink color (pink form) and contains two mononuclear iron sites in different oxidation states: a ferric site (center I) with a distorted tetrahedral sulfur coordination similar to that found in desulforedoxin from Desulfovibrio gigas and a ferrous site (center II) octahedrally coordinated with predominantly nitrogen/oxygen-containing ligands. A new form of desulfoferrodoxin which displays a gray color (gray form) has now been purified. Optical, electron paramagnetic resonance (EPR), and Mössbauer data of the gray desulfoferrodoxin indicate that both iron centers are in the high-spin ferric states. In addition to the EPR signals originating from center I at g = 7.7, 5.7, 4.1, and 1.8, the gray form of desulfoferrodoxin exhibits a signal at g = 4.3 and a shoulder at g = 9.6, indicating a high-spin ferric state with E/D approximately 1/3 for the oxidized center II. Redox titrations of the gray form of the protein monitored by optical spectroscopy indicate midpoint potentials of +4 +/- 10 and +240 +/- 10 mV for centers I and II, respectively. Mössbauer spectra of the gray form of the protein are consistent with the EPR finding that both centers are high-spin ferric and can be analyzed in terms of the EPR-determined spin Hamiltonian parameters. The Mössbauer parameters for both the ferric and ferrous forms of center II are indicative of a mononuclear high spin iron site with octahedral coordination and predominantly nitrogen/oxygen-containing ligands. Resonance Raman studies confirm the structural similarity of center I and the distorted tetrahedral FeS4 center in desulforedoxin and provide evidence for one or two cysteinyl-S ligands for center II. On the basis of the resonance Raman results, the 635 nm absorption band that is responsible for the gray color of the oxidized protein is assigned to a cysteinyl-S-->Fe(III) charge transfer transition localized on center II. The novel properties and possible function of center II are discussed in relation to those of mononuclear iron centers in other enzymes.

Identification of the EPR-active iron-nitrosyl complexes in mammalian ferritins

This study was undertaken to characterize the nitric oxide complexes of mammalian ferritin and their EPR properties to gain a better understanding of the interaction of NO with non-heme iron proteins within the cell. Measurements were made with horse spleen apo- and holoferritins, with chemically modified proteins, and with recombinant human H-chain apoferritin and its site-directed mutants. Three types of EPR signals (A, B, and C) have been identified and attributed to iron-nitrosyl complexes at imidazole groups of histidine, thiol groups of cysteine, and carboxylate groups of aspartate and glutamate, respectively. The C-type axial spectrum has features at g perpendicular' = 4 and g parallel' = 2 characteristic of a paramagnetic Fe(3+)-NO- complex with total spin S = 3/2 and probably arises from nonspecific binding to carboxylate groups on the protein. The S = 1/2 axial B-type signal g perpendicular' = 2.033 and g parallel' = 2.014) is formed at Cys-130 (human H-chain sequence numbering). His-128 and possibly His-118 are sites of formation of the rhombic S = 1/2 A-type complex (gx' = 2.055, gy' = 2.033, and gz' = 2.015); the former residue perhaps plays a role in the conformational stability of the protein as well as in iron binding. The data reveal that the residues Cys-130 and His-128 in the vicinity of 3-fold channels leading to the interior of the protein shell are important in iron-nitrosyl complex formation in mammalian ferritins.

Resonance Raman spectroscopic evidence for the FeS4 and Fe-O-Fe sites in rubrerythrin from Desulfovibrio vulgaris

Resonance Raman (RR) spectra of the non-heme iron protein rubrerythrin from Desulfovibrio vulgaris unequivocally demonstrate the presence of both a rubredoxin-type FeS4 site and a (mu-oxo)diiron(III) cluster. The RR spectra of rubrerythrin excited at 496.5 and 568.2 nm are dominated by bands similar to those of rubredoxin and conform to the vibrational pattern expected for a distorted FeS4 tetrahedron of an Fe(S-Cys)4 site. Numerous overtone and combination bands of the Fe-S stretches are also observed, and a band at 650 cm-1 is assigned to a cysteine C-S stretching mode. The 374-, 355-, and 340-cm-1 bands, assigned to the three components of the v3(T2) asymmetric FeS4 stretching mode, are 2-8 cm-1 lower than the corresponding frequencies for the Desulfovibrio gigas rubredoxin FeS4 site. Similar differences in frequencies of bands assigned to SFeS bending modes between rubredoxin and rubrerythrin are also detected. These frequency differences imply either slightly weaker Fe-S bonds or subtle conformational differences among the cysteinyl ligands in the rubrerythrin versus rubredoxin FeS4 sites. The RR spectrum of rubrerythrin excited at 406.7 nm shows dramatically diminished intensities of the FeS4 bands with concomitant enhancement of a band at 514 cm-1. This band shifts 18 cm-1 to lower frequency when the protein is dissolved in H(2)18O. The frequency of this band and the 18O isotope shift are those expected for the symmetric Fe-O-Fe stretch of a bent oxo-bridged diiron(III) cluster and indicate that this cluster has at least one additional bridging ligand.(ABSTRACT TRUNCATED AT 250 WORDS)

An iron-sulfur center essential for transcriptional activation by the redox-sensing SoxR protein

The soxRS oxidative stress regulon of Escherichia coli is triggered by superoxide (O2.-) generating agents or by nitric oxide through two consecutive steps of gene activation. SoxR protein has been proposed as the redox sensing gene activator that triggers this cascade of gene expression. We have now characterized two forms of SoxR: Fe-SoxR contained non-heme iron (up to 1.6 atoms per monomer); apo-SoxR was devoid of Fe or other metals. The spectroscopic properties of Fe-SoxR indicated that it contains a redox active iron-sulfur (FeS) cluster that is oxidized upon extraction from E. coli. Fe-SoxR and apo-SoxR bound the in vivo target, the soxS promoter, with equal affinities and protected the same region from DNase I in vitro. However, only Fe-SoxR stimulated transcription initiation at soxS in vitro > 100-fold, similar to the activation of soxS expression in vivo. This stimulation occurred at a step after the binding of RNAP and indicates a conformational effect of oxidized Fe-SoxR on the soxS promoter. The variable redox state of the SoxR FeS cluster may thus be employed in vivo to modulate the transcriptional activity of this protein in response to specific types of oxidative stress.

A non-heme iron protein with heme tendencies: an investigation of the substrate specificity of thymine hydroxylase

Thymine hydroxylase from Rhodotorula glutinis catalyzes the oxidation of thymine to its alcohol, aldehyde, and carboxylic acid in three successive reactions. Each step involves stoichiometric consumption of O2 and alpha-ketoglutarate and formation of CO2 and succinate. Given the promiscuity of this enzyme, it was hoped that it would serve as a prototype for understanding the mechanism of this class of enzymes, the non-heme Fe2+ dioxygenases. Kinetic parameters for thymine, O2, Fe2+, and alpha-ketoglutarate have been determined, and isotope effect analysis of (trideuteriomethyl)thymine with enzyme reveals D(V) = 2.08 and D(V/K) = 1.11 at saturating O2. The kinetic parameters for (hydroxymethyl)uracil oxidation have been determined, and incubation of (5'-R)- and (5'-S)-[5'-2H]-5-(hydroxymethyl)uracil with enzyme reveals stereospecific removal of the pro-S hydrogen. No apparent isotope effect is observed in this reaction. The substrate specificity of this enzyme has been examined in detail. The enzyme can catalyze epoxidation, oxidation of a thioether to a sulfoxide and a sulfone, hydroxylation of an unactivated carbon-hydrogen bond, and oxidation of a methylamine to formaldehyde, as revealed through studies with 5-vinyluracil, 5-(methylthio)uracil, 5,6-dihydrothymine, and 1-methylthymine, respectively. In each case, the products were identified by gas chromatography-mass spectrometry, and 18O2-labeling studies revealed that one atom from O2 is incorporated into each product. The enzyme has also been shown to catalyze an uncoupling of hydroxylation and decarboxylation in the presence of a substrate analog incapable of undergoing hydroxylation or a substrate that is difficult to oxidize.(ABSTRACT TRUNCATED AT 250 WORDS)

Evidence for retention of biological activity of a non-heme iron enzyme adsorbed on a silver colloid: a surface-enhanced resonance Raman scattering study

The structure and catalytic properties of the enzyme (E) chlorocatechol dioxygenase (CCD) adsorbed on a citrate-reduced silver colloid are analyzed by surface-enhanced resonance Raman spectroscopy (SERRS). This is the first SERRS study of a non-heme metalloenzyme. It is demonstrated that the native conformation of CCD is retained in the adsorbed state by comparison of resonance Raman scattering (RRS) from CCD in solution with SERRS from CCD adsorbed on the silver colloid. Both spectra show clear evidence of vibrational bands typical of iron-tyrosinate proteins. Furthermore, it is demonstrated that adsorbed CCD retains 60-85% of its enzymatic activity in the reaction of catechol substrate (S) with O2 to give the dioxygenated product (P) cis,cis-muconate. This is accomplished by enzyme assays of Ag-adsorbed CCD and comparison of the SERRS of Ag-adsorbed enzyme-substrate (ES) complex under anaerobic conditions with that of Ag-adsorbed ES in the presence of dioxygen. The SERRS difference spectrum, ES(aerobic)--ES(anaerobic), shows clear evidence for the appearance of the vibrational modes of adsorbed product. The analogous SERR difference spectroscopy experiment is also carried out for the enzyme-inhibitor (EI) complex of CCD with tetrachlorocatechol (TCC). Slow turnover of CCD-TCC is observed by SERRS on exposure to dioxygen which is consistent with the slow rate of turnover of TCC by CCD in solution.

Molecular characterization of flavanone 3 beta-hydroxylases. Consensus sequence, comparison with related enzymes and the role of conserved histidine residues

A heterologous cDNA probe from Petunia hybrida was used to isolate flavanone-3 beta-hydroxylase-encoding cDNA clones from carnation (Dianthus caryophyllus), china aster (Callistephus chinensis) and stock (Matthiola incana). The deduced protein sequences together with the known sequences of the enzyme from P. hybrida, barley (Hordeum vulgare) and snapdragon (Antirrhinum majus) enabled the determination of a consensus sequence which revealed an overall 84% similarity (53% identity) of flavanone 3 beta-hydroxylases from the different sources. Alignment with the sequences of other known enzymes of the same class and to related non-heme iron-(II) enzymes demonstrated the strict genetic conservation of 14 amino acids, in particular, of three histidines and an aspartic acid. The conservation of the histidine motifs provides strong support for the possible conservation of structurally similar iron-binding sites in these enzymes. The putative role of histidines as chelators of ferrous ions in the active site of flavanone 3 beta-hydroxylases was corroborated by diethyl-pyrocarbonate modification of the partially purified recombinant Petunia enzyme.

Characterization of the non-heme iron center of human 5-lipoxygenase by electron paramagnetic resonance, fluorescence, and ultraviolet-visible spectroscopy: redox cycling between ferrous and ferric states

Purified human 5-lipoxygenase, a non-heme iron containing enzyme, has been characterized by electron paramagnetic resonance, (EPR), ultraviolet (UV)-visible and fluorescence spectroscopy. As isolated, the enzyme is largely in the ferrous state and shows a weak X-band EPR signal extending from 0 to 700 G at 15 K, tentatively ascribed to integer spin Fe(II). Titration of the protein with 13-HPOD (13-hydroperoxyoctadecadienoic acid) generates a strong multicomponent EPR signal in the g' approximately 6 region, a yellow color associated with an increased absorption between 310 and 450 nm (epsilon 330nm = 2400 M-1 cm-1), and a 17% decrease in the intrinsic protein fluorescence. The multiple component nature of the g' approximately 6 signal indicates that the metal center in its oxidized state exists in more than one but related forms. The g' approximately 6 EPR signal and the yellow color reach a maximum when approximately 1 mol of 13-HPOD is added/mol of iron; the resultant EPR spectrum accounts quantitatively for all of the iron in the protein with a signal at g' = 4.3 representing less than 3% of the total iron in the majority of samples. Addition of a hydroxyurea reducing agent abolished the g' approximately 6 signal and yellow color of the protein and also reversed the decrease in fluorescence caused by the oxidant 13-HPOD. The results indicate that the g' approximately 6 EPR signal, the yellow color, and the decreased fluorescence are associated with the formation of the Fe(III) form of the enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)

Spectroscopic characterization of 57Fe-reconstituted rubrerythrin, a non-heme iron protein with structural analogies to ribonucleotide reductase

Rubrerythrin, a contraction of rubredoxin and hemerythrin, is the trivial name given to a non-heme iron protein isolated from Desulfovibrio vulgaris (Hildenborough). This protein, whose physiological function is unknown, was first characterized by J. LeGall et al. [(1988) Biochemistry 28, 1636] as being a homodimer of subunit M(r) = 21,900 with four Fe per homodimer distributed as two rubredoxin-type FeS4 centers and one hemerythrin-type diiron cluster. Subsequent analysis of the amino acid sequence of the rubrerythrin gene [Kurtz, D. M., Jr., & Prickril, B.C. (1991) Biochem. Biophys. Res. Commun. 181, 137] revealed an internal homology which suggested that each subunit can accommodate one diiron cluster. Here, we report a procedure for reconstitution of the as-isolated D. vulgaris rubrerythrin with 57Fe. The reconstituted protein was characterized by optical, electron paramagnetic resonance, and Mössbauer spectroscopies. The results indicate successful incorporation of 57Fe into the two types of sites and strongly suggest that each subunit of rubrerythrin can indeed accommodate one diiron cluster as well as one rubredoxin-type center. Combined with amino acid sequence analysis, the spectroscopic characterization further suggests that the rubrerythrin subunit contains a diiron site whose structure is more closely related to that in ribonucleotide reductase than to that in hemerythrin.

Purification and properties of the apple fruit ethylene-forming enzyme

The enzyme that oxidatively converts 1-aminocyclopropanecarboxylic acid (ACC) to ethylene, a key plant growth hormone, has been classified, on the basis of a comparison of homologous protein sequences (derived from the cDNA sequences), as a member of a family of non-heme iron proteins that includes plant and bacterial oxidative enzymes. This knowledge has facilitated the purification of the relatively abundant ethylene-forming enzyme to homogeneity from apple tissue. The properties of the enzyme are consistent with two other recent reports that describes its purification by different protocols, lending credence to the assertion that the key protein has been isolated. New characterizations of the protein have been conducted. Electrospray mass spectrometry shows that its molecular weight (35 331.8 +/- 5 amu) is approximately 50 amu higher than that predicted from the cDNA sequence, identifying the blocking group at the N-terminus as acetyl. The enzyme is activated by bicarbonate at low concentration but is inhibited at high concentration, with the maximum activation occurring at 5 mM. The iron concentration leading to half-maximal activity is 1 microM. The enzyme self-inactivates during turnover. The availability of the purified enzyme will permit definitive studies of the mechanism by which ethylene is produced and provide opportunities to discover molecules that inhibit the process.

Expression of rat liver phenylalanine hydroxylase in insect cells and site-directed mutagenesis of putative non-heme iron-binding sites

Rat liver phenylalanine hydroxylase was expressed in both Escherichia coli and the Spodoptera frugiperda insect cell line, Sf9. Recombinant enzyme from E. coli was inactive and contained less than 0.1 iron atom/subunit. In contrast, recombinant enzyme expressed in Sf9 cells using a baculovirus vector was active and identical in several properties to phenylalanine hydroxylase from rat liver: the Km for 6-methyltetrahydropterin was 39 microM (compared with 35 microM for the rat liver enzyme), 1 atom of iron was "associated" per enzyme subunit, and electron paramagnetic resonance spectra showed that iron was distributed within two distinct environments. Putative iron-binding sites of phenylalanine hydroxylase were studied by mutating either histidine 284 or 289 to serine and expressing these mutant enzymes (PAH-H284S and PAH-H289S) in Sf9 cells. Mutants were expressed at levels similar to wild-type PAH, but contained < or = 0.1 iron/subunit and were inactive. Thus, both His284 and His289 apparently are required for iron binding and hydroxylation activity.

Purification of a cytochrome b containing H2:heterodisulfide oxidoreductase complex from membranes of Methanosarcina barkeri

The reduction of CoM-S-S-HTP, the heterodisulfide of coenzyme M (H-S-CoM) and N-7-mercaptoheptanoylthreonine phosphate (H-S-HTP), with H2 is an energy-conserving step in methanogenic archaea. We report here that in Methanosarcina barkeri this reaction is catalyzed by a membrane-bound multienzyme complex, designated H2:heterodisulfide oxidoreductase complex, which was purified to apparent homogeneity. The preparation was found to be composed of nine polypeptides of apparent molecular masses 46 kDa, 39 kDa, 28 kDa, 25 kDa, 23 kDa, 21 kDa, 20 kDa, 16 kDa, and 15 kDa and to contain 3.2 nmol cytochrome b, 70 to 80 nmol non-heme iron and acid-labile sulfur, 5 nmol Ni, and 0.6 nmol FAD per mg protein. The 23 kDa polypeptide possessed heme-derived peroxidase activity indicating that this polypeptide is the cytochrome b. The purified H2:heterodisulfide oxidoreductase complex catalyzed the reduction of CoM-S-S-HTP with H2 at a specific activity of 6 U/mg protein (1 U = 1 mumol.min-1), the reduction of benzylviologen with H2 at a specific activity of 66 U/mg protein and the reduction of CoM-S-S-HTP benzylviologen with H2 at a specific activity of 66 U/mg protein and the reduction of CoM-S-S-HTP HTP with reduced benzylviologen at a specific activity of 24 U/mg protein. The complex did not mediate the reduction of coenzyme F420 with H2 nor the oxidation of reduced coenzyme F420 with CoM-S-S-HTP. The reduced cytochrome b in the enzyme complex could be oxidized by CoM-S-S-HTP and re-reduced by H2. The specific rates of cytochrome oxidation and reduction were too high to be resolved under our experimental conditions. The findings suggest that the H2:heterodisulfide oxidoreductase complex is composed of a F420-non-reducing hydrogenase, a cytochrome b and heterodisulfide reductase and that cytochrome b is a redox carrier in the electron transport chain involved in CoM-S-S-HTP reduction with H2.

Purification and properties of N5-methyltetrahydromethanopterin:coenzyme M methyltransferase from Methanobacterium thermoautotrophicum

N5-Methyltetrahydromethanopterin:coenzyme M meth-yltransferase is an integral membrane protein found in methanogenic archaea. It catalyzes an energy-conserving step in methane formation from CO2 and from acetate. The enzyme from Methanobacterium thermoautotrophicum (strain Marburg) has been purified 30-fold to apparent homogeneity. The purified enzyme had an apparent molecular mass of 670 kDa and was composed of seven different polypeptides of 34 kDa, 28 kDa, 24 kDa, 23 kDa, 21 kDa, 13 kDa, and 12 kDa. The N-terminal amino acid sequences of these polypeptides were determined. The native 670-kDa enzyme was found to contain 7.6 mol 5-hydroxybenzimidazolyl cobamide/mol, 37 mol non-heme iron/mol and 34 mol acid-labile sulfur/mol. Cobalt analyses after sodium dodecyl sulfate/polyacrylamide gel electrophoresis revealed that the corrinoid was bound to the 23-kDa polypeptide. The apparent molecular masses of the polypeptides given above were determined by sodium dodecyl sulfate/polyacrylamide gel electrophoresis without boiling the samples prior to analysis. When the samples were boiled, as is usually done, the 23-kDa polypeptide changed its apparent molecular mass to 33 kDa and the 21-kDa, 24-kDa, and 28-kDa polypeptides formed aggregates. The specific activity (apparent Vmax) of the purified methyltransferase preparation was 11.6 mumol.min-1.mg protein-1. The apparent Km for N5-methyltetrahydromethanopterin was 260 microM and that for coenzyme M was 60 microM. The preparation was absolutely dependent on the presence of Ti(III) for activity. ATP enhanced the activity 1.5-2-fold.

Rapid purification of rabbit reticulocyte lipoxygenase for electron paramagnetic spectroscopy characterization of the non-heme iron

An efficient three-step purification technique has been developed for the reticulocyte 15-lipoxygenase from rabbit. Ammonium sulfate fractionated reticulocyte lysate was purified by size exclusion chromatography and preparative scale isoelectric focusing. The entire procedure was complete in less than eight hours and was carried out in batches which typically yielded 10 mg of purified enzyme. The identity and purity of the enzyme were evaluated by N-terminal sequencing, sodium dodecylsulfate polyacrylamide gel electrophoresis and specific activity determinations. The enzyme contained approximately one g-atom iron per mole of protein. The iron was present in an electron paramagnetic spectroscopy (EPR) silent, presumably high spin iron(II), form in the isolated enzyme. Treatment with one equivalent of 13-hydroperoxy-9(Z),11(E)-octadecadienoic acid resulted in the appearance of an EPR signal around g6.

Investigation of the mechanism of non-turnover-dependent inactivation of purified human 5-lipoxygenase. Inactivation by H2O2 and inhibition by metal ions

Human 5-lipoxygenase is a non-heme iron protein which is reported to be highly unstable in the presence of oxygen. The results of this investigation demonstrate that H2O2 generated during air oxidation of thiols is the main factor in non-turnover-dependent inactivation of purified recombinant human 5-lipoxygenase for the following reasons: catalase protects against oxygen-dependent inactivation of the enzyme in the presence of dithiothreitol; the active, stable enzyme can be prepared under aerobic conditions with the exclusion of dithiothreitol and contaminating metal ions; 10 microM H2O2 causes the rapid inactivation of the enzyme. The native (ferrous) enzyme is approximately seven times more sensitive to inactivation by H2O2 than the ferric enzyme, suggesting that the mechanism of inactivation involves a Fenton-type reaction of the ferrous enzyme with H2O2, resulting in the formation of an activated oxygen species. Purification of 5-lipoxygenase under aerobic conditions (no dithiothreitol) results in an increase in both the specific activity of the purified protein [up to 70 mumol 5(S)-hydroperoxy-6-trans-8, 11, 14-cis-icosatetraenoic acid (5-HPETE)/mg protein] and in the ratio of specific activity to enzyme iron content compared to enzyme purified under anaerobic conditions in the presence of dithiothreitol. The reaction of the highly active 5-lipoxygenase enzyme shows a dependence on physiological intracellular calcium concentrations, half-maximal product formation being obtained at 0.9 microM free Ca2+. The maximal enzyme activity is also dependent on EDTA and dithiothreitol and low amounts of carrier protein, as well as the known activators PtdCho and ATP. Ca2+ can be substituted by Mn2+, Ba2+ and Sr2+, although lower levels of stimulation are obtained. 5-Lipoxygenase is strongly inhibited by low concentrations (< or = 10 microM) of Zn2+ and Cu2+. The inhibition by Cu2+ is apparently irreversible, whereas that by Zn2+ is slowly reversed (t1/2 = 2 min) in the presence of excess EDTA. These observations on the mechanism of non-turnover-dependent inactivation of 5-lipoxygenase, and the optimisation of assay conditions, have facilitated the purification of large quantities of relatively stable enzyme that will be useful for further kinetic and physical studies.

A molybdenum and a tungsten isoenzyme of formylmethanofuran dehydrogenase in the thermophilic archaeon Methanobacterium wolfei

We have recently reported that the thermophilic archaeon Methanobacterium wolfei contains two formylmethanofuran dehydrogenases, I and II. Formylmethanofuran dehydrogenase II, which is preferentially expressed in tungsten-grown cells, has been purified and shown to be a tungsten-iron-sulfur protein. We have now purified and characterized formylmethanofuran dehydrogenase I from molybdenum-grown cells and shown that it is a molybdenum-iron-sulfur protein. The purified enzyme, with a specific activity of 27 U/mg protein, was found to be composed of three subunits of apparent molecular mass 64 kDa, 51 kDa, and 31 kDa and to contain per mol 146-kDa molecule approximately 0.23 mol molybdenum, 0.46 mol molybdopterin guanine dinucleotide, and 6.6 mol non-heme iron but no tungsten (< 0.01 mol). The molybdenum enzyme differed from the tungsten enzyme (8 U/mg) in that it catalyzed the oxidation of N-furfurylformamide and formate and was inactivated by cyanide. The two enzymes also differed significantly in the pH optimum, in the apparent Km for the electron acceptor, and in the chromatographic behaviour. The molybdenum enzyme and the tungsten enzyme were similar, however, in that the N-terminal amino acid sequences determined for the alpha and beta subunits were identical up to residue 23, indicating that the two proteins are isoenzymes. The molybdenum enzyme, as isolated, was found to display an EPR signal derived from molybdenum as evidenced by isotope substitution.

Iron-sulfur centers as endogenous blue light sensitizers in cells: a study with an artificial non-heme iron protein

The possible involvement of Fe-S clusters in photodynamic reactions as endogenous sensitizing chromophores in cells has been investigated, by using an artificial non-heme iron protein (ANHIP) derived from bovine serum albumin and ferredoxins isolated from spinach and a red marine algae. Ferredoxins and ANHIP, when exposed to visible light, generate singlet oxygen, as measured by the imidazole plus RNO method. Irradiation with intense blue light of the ANHIP-entrapped liposomes caused severe membrane-damage such as liposomal lysis and lipid peroxidation. In the presence of ANHIP, isocitrate dehydrogenase and fructose-1,6-diphosphatase were photoinactivated by blue light. However, all of these photosensitized reactions were significantly suppressed by a singlet oxygen (1O2) quencher, azide, but enhanced by a medium containing deuterium oxide. Further, the Fe-S proteins with the prosthetic groups destroyed did not initiate the blue light-induced reactions. In addition, the action spectrum for 1O2 generation from ANHIP was very similar to the visible absorption spectrum of Fe-S centers. The results obtained in this investigation appear consistent with the suggestion that Fe-S centers are involved in photosensitization in cells via a singlet oxygen mechanism.

EPR detection of heme and nonheme iron-containing protein nitrosylation by nitric oxide during rejection of rat heart allograft

The paramagnetic molecule nitric oxide (NO), produced from L-arginine by a specific enzyme (NO synthase), has been shown to be involved in a surprising variety of mammalian cellular responses, including the regulation of T cell immunity to alloantigens in vitro. In cytotoxic activated macrophages, NO production results in a characteristic pattern of alteration of iron-containing enzyme function that is mimicked by exposure to NO. Electron paramagnetic resonance (EPR) studies have shown the formation of iron-nitrosyl species during macrophage activation and also during sepsis, indicating that alteration of iron-containing protein function may be the result of the well-documented tendency of NO to bind to metal ions. We have recently shown that the NO synthesis induced during alloantigenic activation of rat splenocytes inhibits lymphocyte proliferation and cytotoxic T-lymphocyte generation. This report demonstrates that iron-nitrosyl EPR signals similar to those observed in macrophages and during sepsis are present in the blood and in the grafted tissue of rats during the rejection of allogeneic (but not syngeneic) heart grafts. These signals are found in the blood and at the site of allograft rejection, but are not found in other tissues (such as spleen and lung), and are obliterated by administration of the immunosuppressant FK506. These results directly demonstrate the formation of iron-nitrosyl complexes during vascularized allograft rejection and suggest that consequent destruction of iron-containing protein function plays an important role in the rejection response.

Molecular cloning and sequencing of a non-haem bromoperoxidase gene from Streptomyces aureofaciens ATCC 10762

A bromoperoxidase gene (bpoT), recently cloned from Streptomyces aureofaciens Tü24, was used as a probe in Southern blot hybridization of total DNA from S. aureofaciens ATCC 10762. A single SstI fragment of 5.4 kb was detected, which was cloned via an enriched gene library into Escherichia coli. The functional bromoperoxidase gene was located on a 2.1 kb BamHI-HindIII fragment by subcloning into S. lividans TK64, using the multicopy plasmid pIJ486. The enzyme was overproduced in S. lividans TK64 (up to 30,000 times compared to S. aureofaciens ATCC 10762) and showed the same electrophoretic and immunological properties as the bromoperoxidase BPO-A2 purified from S. aureofaciens ATCC 10762. DNA sequence analysis revealed an open reading frame encoding a predicted polypeptide with the same M(r) and N-terminal amino acid sequence as the purified subunit of BPO-A2.

Fe(II) oxidation and Fe(III) incorporation by the M(r) 66,000 microsomal iron protein that stimulates NADPH oxidation

In a previous study (Minotti, G., and Ikeda-Saito, M. (1991) J. Biol. Chem. 266, 20011-20017) we demonstrated the existence of a M(r) 66,000 microsomal iron protein (MIP) which stimulates NADPH oxidation by shunting electrons from NADPH-cytochrome P-450 reducase to its bound Fe(III). In the present study, purified MIP was depleted of iron and the apoMIP was examined for its ability to incorporate Fe(III) upon an incubation with Fe(II). It was found that apoMIP had an oxygen-dependent ferroxidase activity coupled with the incorporation of Fe(III). The reconstituted MIP exhibited a Fe(III) content and an NADPH oxidation activity similar to those of native MIP. However, the reconstitution of MIP from apoMIP and Fe(II) had to be performed in the presence of detergents to prevent the formation of protein aggregates and the oxidative incorporation of an iron which could not react with NADPH-cytochrome P-450 reductase. This redox inactive iron was probably bound nonspecifically to artifactual sites formed by the protein aggregates.

Mapping the site(s) of MgATP and MgADP interaction with the nitrogenase of Azotobacter vinelandii. Lysine 15 of the iron protein plays a major role in MgATP interaction

Nitrogenase binds and hydrolyzes 2MgATP yielding 2MgADP and 2Pi for each electron that is transferred from the iron protein to the MoFe protein. The iron protein alone binds but does not hydrolyze 2MgATP or 2MgADP and the binding of these nucleotides is competitive. Iron protein amino acid sequences all contain a putatitive mononucleotide-binding region similar to a region found in other mononucleotide-binding proteins. To examine the role of this region in MgATP interaction, we have substituted glutamine and proline for conserved lysine 15. The amino acid substitutions, K15Q and K15P, both yielded a non-N2-fixing phenotype when the genes coding for them were substituted into the Azotobacter vinelandii chromosome in place of the wild-type gene. The iron protein from the K15Q mutant was purified to homogeneity, whereas the protein from the K15P mutant could not be purified in its native form. Unlike wild-type iron protein, the purified K15Q iron protein showed no acetylene reduction, H2 evolution, or ATP hydrolysis activities when complemented with wild-type MoFe protein. The K15Q iron protein and the normal iron protein had a similar total iron content and both proteins showed the characteristic rhombic EPR signal resulting from the reduced state of the single 4Fe-4S cluster bridging the two subunits. Unlike the wild-type iron protein, addition of MgATP to the K15Q iron protein did not result in the perturbation necessary to change the EPR signal of its 4Fe-4S center from a rhombic to an axial line shape. Also unlike the wild-type iron protein, addition of MgATP to K15Q iron protein in the presence of the iron chelator, alpha,alpha'-dipyridyl, did not result in a time-dependent transfer of iron to the chelator. Thus, even though the K15Q iron protein contains a normal 4Fe-4S center, it does not respond to MgATP like the wild-type protein. Examination of the ability of the K15Q iron protein to bind MgADP showed no change from the wild-type iron protein, but its ability to bind MgATP decreased to 35% of the wild-type protein. Thus, in A. vinelandii iron protein, lysine 15 is not needed for interaction with MgADP but is involved in the binding of ATP, presumably through charge-charge interaction with the gamma-phosphate. Based on the above data, this lysine appears to be essential for the MgATP induced conformational change of wild-type iron protein that is required for activity.(ABSTRACT TRUNCATED AT 400 WORDS)

Mutagenesis studies on the amino acid residues involved in the iron-binding and the activity of human 5-lipoxygenase

Human 5-lipoxygenase contains a non-heme iron essential for its activity. In order to determine which amino acid residues are involved in the iron-binding and the lipoxygenase activity, nine amino acid residues in highly homologous regions among the lipoxygenases were individually replaced by means of site-directed mutagenesis. Mutant 5-lipoxygenases in which His-367 or His-550 was replaced by either Asn or Ala, His-372 by either Asn or Ser, or Glu-376 by Gln were completely devoid of the activity. Though mutants containing an alanine residue instead of His-390 or His-399 lacked the activity, the corresponding asparagine substituted mutants exhibited. The other mutants retained the enzyme activity. These results strongly suggest that His-367, His-372, His-550 and Glu-376 are crucial for 5-lipoxygenase activity and coordinate to the essential iron.

Structure-function relationships among the nickel-containing hydrogenases

The enzymology of the heterodimeric (NiFe) and (NiFeSe) hydrogenases, the monomeric nickel-containing hydrogenases plus the multimeric F420-(NiFe) and NAD(+)-(NiFe) hydrogenases are summarized and discussed in terms of subunit localization of the redox-active nickel and non-heme iron clusters. It is proposed that nickel is ligated solely by amino acid residues of the large subunit and that the non-heme iron clusters are ligated by other cysteine-rich polypeptides encoded in the hydrogenase operons which are not necessarily homologous in either structure or function. Comparison of the hydrogenase operons or putative operons and their hydrogenase genes indicate that the arrangement, number and types of genes in these operons are not conserved among the various types of hydrogenases except for the gene encoding the large subunit. Thus, the presence of the gene for the large subunit is the sole feature common to all known nickel-containing hydrogenases and unites these hydrogenases into a large but diverse gene family. Although the different genes for the large subunits may possess only nominal general derived amino acid homology, all large subunit genes sequenced to date have the sequence R-X-C-X-X-C fully conserved in the amino terminal region of the polypeptide chain and the sequence of D-P-C-X-X-C fully conserved in the carboxyl terminal region. It is proposed that these conserved motifs of amino acids provide the ligands required for the binding of the redox-active nickel. The existing EXAFS (Extended X-ray Absorption Fine Structure) information is summarized and discussed in terms of the numbers and types of ligands to the nickel and the various redox species of nickel defined by EPR spectroscopy. New information concerning the ligands to nickel is presented based on site-directed mutagenesis of the gene encoding the large subunit of the (NiFe) hydrogenase-1 of Escherichia coli. Based on considerations of the biochemical, molecular and biophysical information, ligand environments of the nickel in different redox states of the (NiFe) hydrogenase are proposed.

Factors affecting the mRNA levels for the non-heme iron and effector-binding subunits of ribonucleotide reductase

Ribonucleotide reductase which catalyzes the rate-limiting step in the de novo synthesis of dNTPs is composed of two non-identical protein subunits which are not under coordinate control in terms of synthesis and degradation. The mRNAs for the effector-binding (EB) and non-heme iron (NHI) subunits are likewise not under coordinate control during cell cycle traverse. Inhibitors directed at the specific subunits of ribonucleotide reductase block DNA synthesis. These current studies show that drugs such as IMPY or hydroxyurea which specifically inhibit the NHI subunit cause a marked increase in the steady-state level of the mRNA for the NHI subunit while resulting in a decrease in the level of mRNA for the EB subunit. In cells treated with deoxyadenosine, the patterns of the mRNAs for the NHI and EB subunits were different from those seen in the IMPY- or hydroxyurea-treated cells. Control experiments utilizing inhibitors (aphidicolin or araC) directed at DNA polymerase showed that the pattern of changes in the mRNA levels for the NHI and EB subunits were specific for the reductase inhibitors. These changes in the mRNAs for the NHI and EB subunits may be due to drug-induced alterations in transcription rates and/or degradation rates for the specific mRNAs.

Bovine heart microsomes contain an Mr = 66,000 non-heme iron protein which stimulates NADPH oxidation

Bovine heart microsomes have been found to contain a non-heme iron protein which serves as an electron acceptor for NADPH-cytochrome P-450 reductase and therefore stimulates NADPH oxidation. This protein, tentatively referred to as Microsomal Iron Protein (MIP), has been extracted with Triton N-101 and purified by ion exchange chromatography on CM- and DEAE-celluloses and gel filtration on Sepharose 6B. MIP is an Mr = 66,000 monomer with 17 atoms of Fe(III)/molecule. Incubation with dithionite removes iron from MIP and abolishes the stimulation of NADPH oxidation, but subsequent incubation with nitrilotriacetic-Fe(III) reincorporates iron and restores the stimulation of NADPH oxidation. Oxygen is the ultimate electron acceptor. In the presence of oxygen, the enzymatic reduction of MIP Fe(III) is followed by the reoxidation of Fe(II) at the expense of oxygen, generating superoxide anion and regenerating MIP Fe(III) for the continuous oxidation of NADPH. In the absence of oxygen, electron transfer from the reductase to MIP Fe(III) causes the release of Fe(II), which limits the ability of MIP to serve as an electron acceptor and stimulate NADPH oxidation. The--NH2-terminal of MIP has been sequenced, and no homology has been found with the sequence of other iron storage or transport proteins such as ferritin or transferrin.

[Formation of nitric oxide in animal tissues during inflammatory process]

EPR evidence was obtained that more intensive formation of mononitrosyl non-heme iron complexes with diethyl-dithiocarbamate (DETC) took place in mouse liver when inflammation process was initiated in mice by the lipopolysaccharide isolated from Salmonella typhimurium bacterium wall DETC intraperitoneally injected bound with endogenous non-heme iron resulted with DETC-Fe complex formation. These complexes were as a traps of nitric oxide appeared in animal tissues, and NO-Fe-DETC complexes were observed. Phenazone known as a free radical process inhibitor lowered NO production in animal organism. The free radical processes were suggested to intensify under inflammation reactions and to cause the various amino groups oxidation to nitroso groups which were capable to release free nitric oxide.

Use of the stable isotope, 58Fe, for determining availability of nonheme iron in meals

Because of reluctance to use radioisotopes for studies of iron absorption in children, we have explored the feasibility of using the least abundant stable isotope of iron, 58Fe (natural abundance, 0.322 weight %) in a study of nonheme iron absorption. With a balanced cross-over design, each of 16 school-age children was fed a standardized lunch on 3 consecutive days and, 28 days later, an alternate standardized lunch on 3 consecutive days. The lunch included either a beef patty or a beef-soy patty. The mass isotope ratio, 58Fe/57Fe (MIR58/57), was measured in blood by inductively coupled plasma mass spectroscopy before and 14 days after (i.e. study day 15) consuming the three lunches. The MIR58/57 on study day 15 was used as a baseline value for lunches fed on study days 29, 30, and 31. Incorporation of 58Fe into erythrocytes was greater from the lunch with beef patty than from the lunch with beef-soy patty (geometric mean values 2.02 and 1.05% of the dose, p less than 0.03). Based on the similarity of our results with those obtained in adults with radioisotopes, we conclude that 58Fe is a satisfactory tag for studies of nonheme iron absorption from meals.

Uniformity of liver density and nonheme (storage) iron distribution

The extent of variation in tissue density and hepatic nonheme iron concentration has been examined at autopsy in 21 adult livers. Samples were taken from each liver at inferior and superior sites in the midaxillary, anterior axillary, and midclavicular lines. Histologic examination showed diffuse metastatic carcinoma, cirrhosis, fibrosis, necrosis, steatosis, or congestion in 19 livers; two livers were normal. Density was determined by saline displacement of 0.5- to 1.0-g specimens. Nonheme iron concentration was measured at each site in samples of the size obtained by wedge (0.5 to 1.0 g) and percutaneous needle (0.005 to 0.010 g) biopsy using specially developed chemical assays. Density was uniform within each liver. Despite the inclusion of diseased tissues, the variation in density among the 21 livers was small (coefficient of variation, 1.25%). The mean (+/- 1 SD) hepatic density was 1.051 +/- 0.013 g/mL (range, 1.017 to 1.077 g/mL). Within each liver, the nonheme iron also was uniformly distributed among the six sites. Chemical measurements of nonheme iron concentration were not significantly different in samples of the size obtained by wedge or percutaneous liver biopsy. All the hepatic nonheme iron determinations were below the upper 95% confidence limit of concentrations in adult males (480 micrograms/g). In the absence of focal lesions, the uniformity in hepatic density and nonheme iron distribution supports the assumption of several clinical methods for measuring liver storage iron (wedge and needle biopsy, determination of hepatic magnetic susceptibility, computed tomography, and magnetic resonance imaging) that one sample of liver tissue is representative of the whole organ.

Determination of relative spin concentration in some high-spin ferric proteins using E/D-distribution in electron paramagnetic resonance simulations

Lineshape simulations are presented for the multiple, overlapping X-band electron paramagnetic resonance (EPR) spectra in two non-heme, high-spin iron proteins: phenylalanine hydroxylase (PAH) and diferric transferrin. The aim of the calculations is to determine the fraction of iron contributing to each of the sites visible by EPR. The simulations are limited to the experimentally accessible transitions occurring at g-values greater than 1.7. In both PAH and transferrin, at least one of the iron sites is characterized by the ratio of zero-field splitting parameters, E/D, near 1/3 and a broad, asymmetric lineshape. A distribution in E/D-values is used in the simulations to account for this breadth and asymmetry. To test the E/D-distribution model, experimental X-band spectra of diferric transferrin at several salt concentrations are fit by simulation. In this test, first the low-field features arising from transitions between the lowest Kramers doublet levels are simulated using E/D-distributions for two sites. Second, parameters that provide a good fit for the lowest doublet transitions are shown also to fit the resonance near an effective g-value of 4.3 from the middle Kramers doublet transition. When applied to spectra of PAH in the resting state, the E/D-distribution approach accounts for the intensity of one of the two major species of iron. The other species is characterized by E/D = 0.032, and the spectrum of this portion of the resting enzyme may be simulated using a frequency-swept Gaussian lineshape. Spectra for the enzyme in an inhibitor-saturated state are also simulated. The simulations are consistent with previous biochemical studies that indicate that only the E/D = 0.032 form of iron participates in catalysis.

[Purification and characterization of lathosterol 5-desaturase from rat liver microsomes by cytochrome b5-sepharose affinity column chromatography: evidence for the non-heme iron protein]

Lathosterol 5-desaturase, which catalyzes introduction of a delta 5 bond into lathosterol to form 7-dehydrocholesterol, was purified up to 2000-4000-fold with a 13-18% yield from rat liver microsomes by cytochrome b5-Sepharose affinity chromatography followed by isoelectric focusing. The final enzyme preparation was homogenous as judged by SDS-polyacrylamide gel electrophoresis and a single polypeptide of 65,000 daltons. Furthermore, the two molecular forms with isoelectric points of 6.3 and 9.5 were demonstrated by electrofocusing, though they did not show any significant difference with respect to their enzymatic properties. The desaturase was found to be a non-heme iron protein containing one atom of iron per one molecule of the enzyme. The enzyme activity was inhibited strikingly by iron chelators and cyanide. The decreased enzymatic activity, however, was recovered completely by Fe-ion to the original level, suggesting that the iron was essential for the catalytic activity.

Mitochondrial iron not bound in heme and iron-sulfur centers and its availability for heme synthesis in vitro

Rat liver mitochondrial fractions have previously been shown to contain a pool of iron which was bound neither in cytochromes nor in iron-sulfur centers (Tangerås, A., Flatmark, T., Bãckstrõm, D. and Ehrenberg, A. (1980) Biochim. Biophys. Acta 589, 162-175), and in the present study the availability of this iron pool for heme synthesis has been studied in isolated mitochondria. A minor fraction of this iron is here shown to originate from iron-rich lysosomes present as a contaminant in mitochondrial fractions isolated by differential centrifugation, and a method for the selective quantitation of this iron pool was developed. The availability of the mitochondrial iron pool for heme synthesis by mitochondria in vitro was studied using a recently developed HPLC method for the assay of ferrochelatase activity. When deuteroporphyrin was used as the substrate, 1.04 +/- 0.13 nmol/mg protein of deuteroheme was formed after 6 h incubation at 37 degrees C when a plateau was approached, and the initial rate of heme synthesis was 0.3 nmol/h per mg protein. Heme formation from the physiological substrate protoporphyrin was also seen. The heme synthesis increased with the amount of mitochondria used and was blocked by both Fe(II) and Fe(III) chelators. The heme synthesis was independent of mitochondrial oxidizable substrates and no difference was observed between pH 7.4 and 6.5. FMN slightly stimulated the formation of heme from endogenous iron, probably by mobilization of a small amount of contaminating lysosomal iron present in the preparations. The possibility that the mitochondrial iron pool functions as the proximate iron donor for heme synthesis by ferrochelatase in vivo is discussed.

Covalent modification of the iron protein of nitrogenase from Rhodospirillum rubrum by adenosine diphosphoribosylation of a specific arginine residue

Nitrogenase in Rhodospirillum rubrum is inactivated in vivo by the covalent modification of the Fe protein with a nucleotide. The preparation of two modified peptides derived from proteolytic digestion of the inactive Fe protein is described. The modifying group is shown to be adenosine diphosphoribose, linked through the terminal ribose to a guanidino nitrogen of arginine. The structural features were established by using proton and phosphorus NMR, positive- and negative-ion fast atom bombardment mass spectrometry, and fast atom bombardment/collisionally activated decomposition mass spectrometry. Spectral methods along with chromatographic analysis and sequential degradation established the sequence of the modification site of Fe protein as Gly-Arg(ADR-ribose)-Gly-Val-Ile-Thr. This corresponds to the sequence in the Fe protein from Azotobacter vinelandii for amino acid residues 99 to 104.

On the origin of the non-haemic iron transferrin ESR signal: ESR investigations on histidine-iron-citric acid systems

The nature of the high spin ferric iron complex located at g = 4.3 has been investigated by means of electron spin resonance spectroscopy and polarography. It could be shown that two complexes each exist in the acid and alkaline pH region, and that the iron is bound to two histidines, three citric acids, and probably to one bicarbonate. These results agree well with previous findings according to which the ligand field of iron should be composed mainly of oxygen and nitrogen atoms. Another low-field signal located at g = 3.6 appears in the pH range from 2 to 7 only and exhibits its maximum where the g = 4.3 signal has its minimum. Its exact nature is still unknown but it seems to represent some intermediate state of the ternary Fe3+-histidine-citric acid complex. When citric acid is used, the spin concentration seems to be always larger than in the case of ascorbic acid. Since the effect obtained with ascorbic acid and citric acid seems to be similar, it may be concluded that the biological function of both of the acids might be somehow related to each other.

Biological nitrogen fixation: primary structure of the Rhizobium trifolii iron protein gene

Biological nitrogen fixation in the Rhizobium-legume symbiosis is dependent on the induction of a bacterially-encoded enzyme complex, nitrogenase. To examine the organization and expression of the genes encoding the components of nitrogenase in this complex system, these genes have been isolated from the legume symbiont Rhizobium trifolii by molecular cloning. DNA sequence analysis of the entire nifH gene (encoding the Fe-protein component of nitrogenase) and of the amino-terminal 141 codons of the nifD gene (encoding the alpha-subunit of the Mo-Fe protein) indicates that these genes are linked on a single operon in this strain. The Fe-protein amino acid sequence shares considerable homology with the sequence from other organisms, in particular the related organism Rhizobium meliloti (90% homology). The nif structural genes are preceded by a DNA sequence which is repeated at least three times in the Rhizobium trifolii genome.

A novel iron protein from Desulfovibrio gigas

The isolation, purification, and partial characterization of a novel iron-containing protein from the sulfate-reducing anaerobic bacterium, Desulfovibrio gigas, is described. The highly insoluble protein was isolated from the cell debris following osmotic shock of the bacteria. The insoluble fraction consistently contained about 90% of the cell-associated iron. Elemental analysis of a crude protein preparation gave 5.3% iron, 2.9% sulfur and 11.9% nitrogen. An independent colorimetric iron analysis showed 6.4% iron. The iron could be dissociated from the protein by treatment with 5% SDS. The iron-free protein was purified by a combination of organic extraction and DEAE-cellulose chromatography. The purified protein showed only one major band, Mr 14000, by SDS-polyacrylamide gel electrophoresis. The protein could be reconstituted upon treatment with an appropriate mixture of FeS and beta-mercaptoethanol. The reconstituted protein had the same physical and chemical properties as the native protein. The amino acid composition was not unusual except for the high isoleucine content.