Biomedical subjects

J D Lipscomb

Publications and source records attributed to J D Lipscomb.

At least 37 records · Page 2Linked to original sources

PubMed1997

Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.

Protocatechuate 3,4-dioxygenase (3,4-PCD) utilizes a ferric ion to catalyze the aromatic ring cleavage of 3,4-dihydroxybenzoate (PCA) by incorporation of both atoms of dioxygen to yield beta-carboxy-cis, cis-muconate. The crystal structures of the anaerobic 3,4-PCD.PCA complex, aerobic complexes with two heterocyclic PCA analogs, 2-hydroxyisonicotinic acid N-oxide (INO) and 6-hydroxynicotinic acid N-oxide (NNO), and ternary complexes of 3,4-PCD.INO.CN and 3,4-PCD. NNO.CN have been determined at 2.1-2.2 A resolution and refined to R-factors between 0.165 and 0.184. PCA, INO, and NNO form very similar, asymmetrically chelated complexes with the active site Fe3+ that result in dissociation of the endogenous axial tyrosinate Fe3+ ligand, Tyr447 (147beta). After its release from the iron, Tyr447 is stabilized by hydrogen bonding to Tyr16 (16alpha) and Asp413 (113beta) and forms the top of a small cavity adjacent to the C3-C4 bond of PCA. The equatorial Fe3+ coordination site within this cavity is unoccupied in the anaerobic 3,4-PCD.PCA complex but coordinates a solvent molecule in the 3,4-PCD.INO and 3,4-PCD.NNO complexes and CN- in the 3,4-PCD.INO.CN and 3,4-PCD.NNO.CN complexes. This shows that an O2 analog can occupy the cavity and suggests that electrophilic O2 attack on PCA is initiated from this site. Both the dissociation of the endogenous Tyr447 and the expansion of the iron coordination sphere are novel features of the 3,4-PCD. substrate complex which appear to play essential roles in the activation of substrate for O2 attack. Together, the structures presented here and in the preceding paper [Orville, A. M., Elango, N. , Lipscomb, J. D., & Ohlendorf, D. H. (1997) Biochemistry 36, 10039-10051] provide atomic models for several steps in the reaction cycle of 3,4-PCD and related Fe3+-containing dioxygenases.

Crystallography, X-Ray↗

PubMed1997

Roles of the methane monooxygenase reductase component in the regulation of catalysis.

The reductase component (MMOR) of the soluble methane monooxygenase isolated from Methylosinus trichosporium OB3b catalyzes transfer of 2e- from NADH to the hydroxylase component (MMOH) where oxygen activation and substrate oxidation occur. It is shown here that MMOR can also exert regulatory effects on catalysis by binding to MMOH or to the binary complex of MMOH and component B (MMOB), another regulatory protein. MMOR alters the oxidation-reduction potentials of the dinuclear iron cluster at the active site of MMOH. Although little change is observed in the potential for the first electron transfer to the cluster (E(1)0' = 76 mV), the E(2)0' potential value for the second electron transfer is increased from 21 to 125 mV. This shift provides a larger driving force for electron transfer from MMOR and favors transfer of two rather than one electron as required by catalysis. Similar positive shifts in potential are observed even in the presence of MMOB which has been shown to cause a 132 mV negative shift in the midpoint potential of MMOH in the absence of MMOR. MMOR is also shown to decrease the rate of reaction between the fully reduced MMOH-MMOB and O2 approximately 20-fold at 4 degrees C. However, the time course of the key catalytic cycle intermediate that can react with substates, compound Q, is unaffected. This implies a compensating faster decay of one or more of the intermediates that occur between diferrous MMOH and compound Q in the reaction cycle, thereby limiting potential nonproductive autodecay of these intermediates. Accordingly, an increase in single turnover product yield is observed in the presence of MMOR. Interestingly, MMOR can cause the redox potential increases, changes in rates, and the increase in product yield when present at only 10% of the concentration of MMOH active sites. Substrate binding is shown to induce negligible changes in the redox potentials. Two alternative regulatory schemes are presented based on (i) thermodynamic coupling of component binding and redox changes or (ii) dynamic interconversion of two states of MMOH promoted by MMOR.

Catalysis↗

PubMed1997

Radiolytic reduction of methane monooxygenase dinuclear iron cluster at 77 K. EPR evidence for conformational change upon reduction or binding of component B to the diferric state.

The soluble form of methane monooxygenase (MMO) consists of three components: reductase, hydroxylase (MMOH), and "B" (MMOB). Resting MMOH contains a diferric bis-mu-hydroxodinuclear iron "diamond core" cluster which is the site of oxygen activation chemistry after reduction. Here it is shown that gamma-irradiation of MMOH at 77 K results in reduction of the diiron cluster to an EPR active Fe(II). Fe(III) mixed valence state. At this temperature, the conformation of the enzyme remains essentially unchanged during reduction, so the EPR-spectrum becomes a probe of the conformation of the diferric state. The gamma-irradiated MMOH exhibits EPR spectra that differ in lineshape and saturation properties from those of the mixed valence MMOH generated by chemical reduction in solution; annealing the gamma-irradiated sample at 230 K yields the spectra of the chemically reduced sample. This demonstrates that the conformation of diferric MMOH in the vicinity of the diiron cluster changes during reduction to the mixed valence state. The analogous experiment for the MMOB.MMOH complex gives a new mixed valence species following gamma-irradiation that differs from all previously reported mixed valence species. Thus, binding of MMOB also causes a change in the conformation of diferric MMOH. It is hypothesized that the structural changes observed for the first time here may involve conversion of the dihydroxo-bridged diamond core structure to one with more readily dissociable bridging oxygen ligands to facilitate reaction with O2 following cluster reduction.

Binding Sites↗

PubMed1997

An Fe2IVO2 diamond core structure for the key intermediate Q of methane monooxygenase.

A new paradigm for oxygen activation is required for enzymes such as methane monooxygenase (MMO), for which catalysis depends on a nonheme diiron center instead of the more familiar Fe-porphyrin cofactor. On the basis of precedents from synthetic diiron complexes, a high-valent Fe2(micro-O)2 diamond core has been proposed as the key oxidizing species for MMO and other nonheme diiron enzymes such as ribonucleotide reductase and fatty acid desaturase. The presence of a single short Fe-O bond (1.77 angstroms) per Fe atom and an Fe-Fe distance of 2.46 angstroms in MMO reaction intermediate Q, obtained from extended x-ray absorption fine structure and Mössbauer analysis, provides spectroscopic evidence that the diiron center in Q has an Fe2IVO2 diamond core.

Binding Sites↗

PubMed1997

Crystal structure of the hydroxylase component of methane monooxygenase from Methylosinus trichosporium OB3b.

Methane monooxygenase (MMO), found in aerobic methanotrophic bacteria, catalyzes the O2-dependent conversion of methane to methanol. The soluble form of the enzyme (sMMO) consists of three components: a reductase, a regulatory "B" component (MMOB), and a hydroxylase component (MMOH), which contains a hydroxo-bridged dinuclear iron cluster. Two genera of methanotrophs, termed Type X and Type II, which differ markedly in cellular and metabolic characteristics, are known to produce the sMMO. The structure of MMOH from the Type X methanotroph Methylococcus capsulatus Bath (MMO Bath) has been reported recently. Two different structures were found for the essential diiron cluster, depending upon the temperature at which the diffraction data were collected. In order to extend the structural studies to the Type II methanotrophs and to determine whether one of the two known MMOH structures is generally applicable to the MMOH family, we have determined the crystal structure of the MMOH from Type II Methylosinus trichosporium OB3b (MMO OB3b) in two crystal forms to 2.0 A resolution, respectively, both determined at 18 degrees C. The crystal forms differ in that MMOB was present during crystallization of the second form. Both crystal forms, however, yielded very similar results for the structure of the MMOH. Most of the major structural features of the MMOH Bath were also maintained with high fidelity. The two irons of the active site cluster of MMOH OB3b are bridged by two OH (or one OH and one H2O), as well as both carboxylate oxygens of Glu alpha 144. This bis-mu-hydroxo-bridged "diamond core" structure, with a short Fe-Fe distance of 2.99 A, is unique for the resting state of proteins containing analogous diiron clusters, and is very similar to the structure reported for the cluster from flash frozen (-160 degrees C) crystals of MMOH Bath, suggesting a common active site structure for the soluble MMOHs. The high-resolution structure of MMOH OB3b indicates 26 consecutive amino acid sequence differences in the beta chain when compared to the previously reported sequence inferred from the cloned gene. Fifteen additional sequence differences distributed randomly over the three chains were also observed, including D alpha 209E, a ligand of one of the irons.

Amino Acid Sequence↗

PubMed1997

Cloning, overexpression, and mutagenesis of the gene for homoprotocatechuate 2,3-dioxygenase from Brevibacterium fuscum.

Homoprotocatechuate (hpca, 3,4-dihydroxyphenylacetate) is a central intermediate for the bacterial degradation of aromatic compounds. Homoprotocatechuate 2,3-dioxygenase (HPCD) catalyzes the key ring cleavage step in the metabolism of hpca by the Gram (+) bacterium Brevibacterium fuscum to yield alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. A genomic DNA library of B. fuscum was constructed in Escherichia coli using a cosmid vector and screened by spraying the cells with hpca. One clone was found to contain the gene for HPCD based on its ability to convert hpca into the yellow-colored product. This cosmid clone was further subcloned and the gene for HPCD was localized and sequenced. The open reading frame codes for a protein with 365 amino acids and M(r) = 41,699, in accord with the characteristics of the previously purified wild-type enzyme. The gene for HPCD was overexpressed in E. coli to approximately 30% of the total soluble protein, and purification of the recombinant enzyme to apparent homogeneity was achieved by a two-step procedure. Iron was the only abundant metal found in the purified recombinant enzyme, and the specific activity per iron was comparable to that observed for the wild-type enzyme. The deduced amino acid sequence of HPCD has a very high level of homology (78.6% identity in the 337-aa overlap) to the manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) from Arthrobacter globiformis CM-2. The basis for the difference in metal selection by HPCD and MndD was investigated by mutagenesis of a 50-base-pair region of the HPCD gene containing three frame shifts relative to the MndD gene. The purified triple mutant of HPCD did not exhibit a significant change in the metal content; therefore, other factors must contribute to the selection of the active site metal.

3,4-Dihydroxyphenylacetic Acid↗

PubMed1996

Large kinetic isotope effects in methane oxidation catalyzed by methane monooxygenase: evidence for C-H bond cleavage in a reaction cycle intermediate.

The reduced hydroxylase component (MMOH) of soluble methane monooxygenase (MMO) from Methylosinus trichosporium OB3b reacts with O2 and CH4 to produce CH3OH and H2O in a single-turnover reaction. Transient kinetic analysis of this reaction has revealed at least five and probably six intermediates during the turnover [Lee, S.-K., Nesheim, J. C., & Lipscomb, J. D. (1993) J. Biol. Chem. 268, 21569-21577; Liu, Y., Nesheim, J. C., Lee, S.-K., & Lipscomb, J. D. (1995) J. Biol. Chem. 270, 24662-24665]. One intermediate, termed compound Q, reacts with CH4 to yield enzyme-bound product. It is shown here that the deuterium kinetic isotope effect (KIE) for the reaction of compound Q with CH4 is 50-100, which is one of the largest effects observed to date. The rate constants for the reactions of the deuterated homologs of methane decrease monotonically as the deuterium content increases, suggesting that a large primary isotope effect dominates. The KIEs determined by analyzing the products after a single turnover have the following values: 1:1 CH4:CD4 (19); CD3H (12); CD2H2 (9); and CH3D (4). The KIE values determined by directly observing the reactive intermediate and by monitoring product ratios are all large, consistent with complete C-H bond breaking in the oxygenation step of the reaction. However, the differences in the KIE values determined by these two methods suggest that the reaction is more complex than currently proposed. A modified mechanism introducing the possibility of hydrogen-atom reabstraction by an intermediate methyl radical is proposed.

Computer Simulation↗

PubMed1996

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 alpha-hydroxy- delta-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 alpha4 and alpha6 (alpha subunit Mr = 42500 +/- 1500) and binds approximately 1 Fe(II)/subunit. Although the substrate Km 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/vi 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.

Amino Acids↗

PubMed1995

Gating effects of component B on oxygen activation by the methane monooxygenase hydroxylase component.

Component B (MMOB) of the soluble methane monooxygenase (MMO) system accelerates the initial velocity of methane oxidation by up to 150-fold by an unknown mechanism. The active site of MMO contains a diferric, hydroxo-bridged diiron cluster located on the hydroxylase component (MMOH). This cluster is reduced by the NAD(P)H-coupled reductase component to the diferrous state, which then reacts with O2 to yield two reaction cycle intermediates sequentially termed compounds P and Q. The rate of compound P formation is shown here to be independent of O2 concentration, suggesting that an MMOH-O2 complex (compound O) is (congruent to irreversibly) formed before compound P. Compound Q is capable of reacting with hydrocarbons to yield the MMOH-product complex, compound T. It is shown here that MMOB accelerates catalysis by increasing congruent to 1000-fold the rate of O2 association and reaction with diferrous MMOH leading to compound P. Modeling of the single turnover reaction in the presence of substoichiometric MMOB suggests that MMOB also accelerates the compound P to Q conversion by congruent to 40-fold. Due to this O2-gating effect of MMOB, either compound Q or T becomes the dominant species during turnover, depending upon the substrate concentration and type. Because these are the species that either react with substrate (Q) or release product (T), their buildup maximizes the turnover rate. This is the first direct role in catalysis to be recognized for MMOB and represents a novel method for oxygenase regulation.

Kinetics↗

PubMed1995

X-ray absorption spectroscopic studies of the Fe(II) active site of catechol 2,3-dioxygenase. Implications for the extradiol cleavage mechanism.

The extradiol-cleaving catechol 2,3-dioxygenase (2,3-CTD) isolated from Pseudomonas putida mt-2 and its catechol and ternary E.S.NO complexes are characterized by X-ray absorption spectroscopy (XAS). The intensities of the 1s-->3d transitions in the pre-edge spectra of the uncomplexed enzyme and its substrate complex show that the Fe(II) center is five-coordinate in both complexes, in agreement with earlier magnetic circular dichroism studies [Mabrouk, P. A., Orville, A. M., Lipscomb, J. D., & Solomon, E. I. (1991) J. Am. Chem. Soc. 113, 4053-4061]. Analysis of the EXAFS region of uncomplexed 2,3-CTD shows five N/O ligand atoms 2.09 A from the active site Fe(II). In the 2,3-CTD.catechol complex, one N/O atom is located at 1.93 A and four N/O type ligands are at 2.10 A. By comparison with [FeII-(6TLA)(DBCH)](ClO4), the first well-characterized mononuclear Fe(II).catechol model complex, the 1.93 A scatterer is proposed to be the oxygen from the deprotonated hydroxyl group of the coordinated catecholate monoanion. Nitric oxide binds to the Fe(II) center in the enzyme.catechol complex without displacing the existing ligands, resulting in the formation of a six-coordinate complex, as indicated by the addition of a new N/O type scatterer at 1.74 A. Bond valence sum (BVS) analysis of the bond lengths derived from the EXAFS fits gives values that correspond to the iron oxidation states established for these complexes, thus lending credence to the coordination environment deduced for the iron center in those complexes. The present study provides the first evidence for a monoanionic substrate binding mode in an extradiol dioxygenase, which is distinct from the dianionic binding mode proposed for intradiol dioxygenases. We speculate that this difference in binding mode may have important ramifications for the site of aromatic ring cleavage in the subsequent oxygen insertion reactions.

Binding Sites↗

PubMed1994

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.

Amino Acid Sequence↗

PubMed1994

Preliminary crystallographic study of protocatechuate 3,4-dioxygenase from Brevibacterium fuscum.

The enzyme protocatechuate 3,4-dioxygenase from the Gram positive organism Brevibacterium fuscum crystallizes in the triclinic space group P1 with unit cell dimensions a = 96.1 A, b = 97.2 A, c = 118.1 A and alpha = 113.9 degrees, beta = 90.7 degrees, gamma = 117.8 degrees. The rod-like crystals diffract to 2.4 A resolution. Rotation function analysis suggests that there are six promoters arranged with local 32 symmetry in the asymmetric unit rather than the previously proposed pentameric complex.

Brevibacterium↗

PubMed1994

Preliminary crystallographic analysis of methane mono-oxygenase hydroxylase from Methylosinus trichosporium OB3b.

The hydroxylase component of the enzyme methane mono-oxygenase from Methylosinus trichosporium OB3b has been crystallized in the orthorhombic space group C222(1) with unit cell dimensions a = 264.5 A, b = 71.2 A, c = 139.4 A. The crystals grow as square, thick plates and diffract to beyond 2 A resolution. There is one half of the hydroxylase dimer in the asymmetric unit.

Crystallization↗

PubMed1994

Oxidation-reduction potentials of the methane monooxygenase hydroxylase component from Methylosinus trichosporium OB3b.

Methane monooxygenase (MMO) isolated from Methylosinus trichosporium OB3b consists of hydroxylase (MMOH), reductase (MMOR), and "B" (MMOB) protein components. MMOH contains two oxygen-bridged dinuclear iron clusters that are the sites of O2 activation and hydrocarbon oxidation. Each cluster can be stabilized in diferric [Fe(III).Fc(III)], mixed-valence [Fe(II).Fe(III)], and diferrous [Fe(II).Fe(II)] redox states. We have correlated the EPR spin quantitation of the S = 1/2 mixed-valence state with the system electrode potential to determine both formal redox potential values for MMOH at 4 degrees C: E1 degrees' = +76 +/- 15 mV and E2 degrees' = +21 +/- 15 mV (Em = +48 mV, 61% maximum mixed-valence state). Complementary Mössbauer studies of 57Fe-enriched MMOH allowed all three redox states to be quantitated simultaneously in individual samples and revealed that the distribution of redox states was in accord with the measured potential values. EPR spectra of partially reduced MMOH showed that the apparent midpoint potential values of MMOH-MMOR, MMOH-MMOR-MMOB, and MMOH-MMOR-MMOB-substrate complexes were slightly more positive than that of MMOH alone. In contrast, the MMOH-MMOB complex appeared to have a substantially more negative redox potential. The formal redox potential values of the latter complex were determined to be E1 degrees' = -52 +/- 15 mV and E2 degrees' = -115 +/- 15 mV, respectively, at 4 degrees C (Em = -84 mV, 65% maximum mixed-valence state). This negative 132-mV shift in the midpoint potential of MMOH coupled to MMOB binding suggests that MMOB binds approximately 10(4) more strongly to the diferric state of MMOH than to the diferrous state. Since the potential shift is strongly negative, and since a nearly constant separation between the two formal potential values of MMOH is maintained when MMOB binds, the role of the MMOB-MMOH complex must not be to thermodynamically stabilize the formation of the diferrous cluster which is the form that reacts with O2 during catalysis. However, MMOB binding may provide kinetic stabilization of the diferrous state and/or modulation of the interaction of MMOH with O2 and hydrocarbon substrates. Such roles may be effected through cyclic association and dissociation of the MMOB-MMOH complex as MMOH oscillates between redox states during catalysis, thereby dynamically altering the affinity of this complex.

Alkenes↗

PubMed1994

Biochemistry of the soluble methane monooxygenase.

The soluble form of methane monooxygenase (MMO) catalyzes the reaction NAD(P)H + O2 + CH4 + H+-->NAD(P)+ + H2O + CH3OH. Many other hydrocarbons serve as adventitious substrates. MMO consists of three protein components: component B, reductase, and hydroxylase (MMOH), the active site of which contains a hydroxo-bridged dinuclear iron cluster that is the site of catalysis. Such a cluster has not been previously associated with oxygenases, and spectroscopic studies have been conducted to ascertain its structural features and accessibility. The mechanism of MMO has been investigated through the use of diagnostic chemical reactions and transient kinetics. Both approaches are consistent with a mechanism in which the diiron cluster is first reduced to the diferrous state and then reacts with O2. The O-O bond is apparently cleaved heterolytically to yield water and an [Fe(IV).Fe(IV)]=O species, which purportedly abstracts a hydrogen atom from methane to yield a substrate radical and a diiron cluster-bound hydroxyl radical. Recombination of the radicals yields the product methanol. An intermediate with the properties of the novel [Fe(IV).Fe(IV)] = O species has been trapped and characterized. This is the first such species to be isolated in biology. Meanwhile, the reductase and component B have roles in catalysis beyond simple electron transfer from NAD(P)H. These roles appear to be related to regulation of catalysis, and are mediated by the formation of specific component complexes that alter the physical and catalytic properties of MMOH at different stages of the turnover cycle.

Models, Chemical↗

PubMed1993

Transient intermediates of the methane monooxygenase catalytic cycle.

Three new intermediates of the catalytic cycle of the soluble form of methane monooxygenase (MMO) isolated from Methylosinus trichosporium OB3b have been detected using transient kinetic techniques. MMO consists of hydroxylase (MMOH), reductase, and "B" (MMOB) components. MMOH contains an oxygen-bridged [Fe(III).Fe(III)] cluster that catalyzes O2 activation and insertion chemistry. At 4 degrees C, rapid mixing of O2 with diferrous MMOH ([Fe(II).Fe(II)]) in the presence of a 2-fold excess of MMOB resulted in loss of the g = 16 EPR signal characteristic of the diferrous cluster at an apparent first order rate of 22 +/- 5 s-1 (O2 approximately 700 microM). Subsequently, an EPR silent, chromophoric (lambda max = 330 and 430 nm, epsilon approximately 7500 M-1 cm-1 at each wavelength) intermediate (compound Q) formed with an average first order rate constant of 1 +/- 0.1 s-1 and then decayed at 0.05 +/- 0.01 s-1. Since compound Q formed much more slowly than diferrous MMOH disappeared, at least one other undetected intermediate (compound P) must have formed before compound Q. MMO substrates had little or no effect on the formation rate of compound Q, but they caused the decay rate to increase linearly with the concentration added. The substrates methane, furan, and nitrobenzene caused compound Q decay to occur with second order rate constants of 19,000 M-1 s-1, 9000 M-1 s-1, and 200 M-1 s-1 (+/- 5%), respectively. When nitrobenzene was used as a substrate, a second chromophoric intermediate (compound T, lambda max = 325 nm, with a shoulder at 395 nm, epsilon 395 approximately 6000 M-1 cm-1) formed at the same rate as compound Q decay. Chemical quench studies showed that compound T is an enzyme-product complex that decays with a rate constant of 0.02 +/- 0.005 s-1. This rate is approximately the same as kcat for nitrobenzene turnover at 4 degrees C catalyzed by the reconstituted MMO system, suggesting that product release is the rate-limiting step in catalysis. The characteristics of compound Q suggest that it may be the activated form of the enzyme that directly catalyzes substrate oxidation.

Binding Sites↗

PubMed1993

Simultaneous binding of nitric oxide and isotopically labeled substrates or inhibitors by reduced protocatechuate 3,4-dioxygenase.

The active site Fe3+ of protocatechuate (PCA) 3,4-dioxygenase can be nonenzymatically reduced to Fe2+, to give a colorless and EPR-silent enzyme (Er). Nitric oxide (NO) binds to Er to yield a species with EPR (S = 3/2; g = 4.341, 3.693, 1.984; E/D = 0.055) and optical absorption (lambda max = 430 nm, epsilon approximately 1870 M-1 cm-1/iron) spectra. Addition of NO to a preformed Er. PCA complex results in a new species (EPR: S = 3/2; g = 4.920, 2.988, 1.846; E/D = 0.175; optical: lambda max = 404 nm, epsilon approximately 3930 M-1 cm-1/iron). Hyperfine broadening from the substrates [17O]PCA or [17O]homoprotocatechuate (HPCA) is observed in the EPR spectra of Er.substrate.NO complexes only when the 17O (I = 5/2) is placed in the carbon-4 OH group, suggesting that only this group binds to the iron when NO is bound. Previous studies (Orville, A. M., and Lipscomb, J. D. (1989) J. Biol. Chem. 261, 8791-8801) showed that both OH groups of HPCA can bind to the Fe3+ of the oxidized enzyme. Thus, the NO may compete with the substrate carbon-3 OH group for a binding site on the Fe2+. In contrast, when either PCA or HPCA is added to a preformed Er.NO complex, no substrate binding to the Fe2+ is detected. At 2.3 K, white light photodissociates NO from the Er.NO and Er.PCA.NO complexes. The Er.NO complex is photodissociated to a greater extent than the Er.PCA.NO complex, and different NO rebinding kinetics are observed showing that the substrate strongly influences the photodissociation/reassociation process. Photodissociation of each complex results in the formation of some Fe3+, suggesting that the nitrosyl complex has at least partial Fe(3+)-NO- character. In solution at 5-10 degrees C, white light promotes conversion of preformed Er.NO plus PCA to the Er.PCA.NO complex, suggesting that formation of the latter complex requires dissociation of NO. It is proposed that initial NO binding blocks the single site for exogenous ligand binding on the iron, thereby inhibiting PCA association. In contrast, PCA binding before NO appears to evoke an enzyme conformational change that allows simultaneous NO binding in another ligand site. These results are consistent with the current model for the mechanism of intradiol dioxygenases in which a PCA-induced conformational change allows substrate to bind as an Fe3+ chelate and O2 reacts initially with the PCA rather than the Fe3+.

Binding Sites↗

PubMed1993

Purification and characterization of protocatechuate 2,3-dioxygenase from Bacillus macerans: a new extradiol catecholic dioxygenase.

Protocatechuate 2,3-dioxygenase (2,3-PCD) from Bacillus macerans JJ1b has been purified to homogeneity for the first time. The enzyme catalyzes proximal extradiol ring cleavage of protocatechuate (PCA) with the attendant incorporation of both atoms of oxygen from O2. The holoenzyme has a mass of 143 +/- 7 kDa as determined by ultracentrifugation and other techniques. It is composed of four apparently identical subunits with M(r)s of 35,500, each containing one iron atom. Mössbauer spectroscopy of 57Fe-enriched enzyme showed that the irons are indistinguishable and are high spin (S = 2) Fe2+ in both the uncomplexed and substrate-bound enzyme. However, the quadrupole splitting, delta EQ, and isomer shift, delta, of the Mössbauer spectrum changed from delta EQ = 2.57 mm/s and delta = 1.29 mm/s to delta EQ = 2.73 mm/s and delta = 1.19 mm/s upon PCA binding to the enzyme, showing that the iron environment is altered when substrate is present. The enzyme was also found to bind variable and substoichiometric amounts of Mn2+, but this metal could be removed without loss of activity or stability. The inherently electron paramagnetic resonance (EPR)-silent Fe2+ of the enzyme reversibly bound nitric oxide to produce an EPR-active species (g = 4.11, 3.95; S = 3/2). The specific activity of the enzyme was found to be correlated with the amount of the S = 3/2 species formed, showing that activity is dependent on Fe2+. Anaerobic addition of substrates to the enzyme-nitric oxide complex significantly altered the EPR spectrum, suggesting that substrates bind to or near the iron. The enzyme was inactivated by reagents that oxidize the Fe2+, such as H2O2 and K3FE(CN)6; full activity was restored after reduction of the iron by ascorbate. Steady-state kinetic data were found to be consistent with an ordered bi-uni mechanism in which the organic substrate must add to 2,3-PCD before O2. The enzyme has the broadest substrate range of any of the well-studied catecholic dioxygenases. All substrates have vicinal hydroxyl groups on the aromatic ring except 4-NH2-3-hydroxybenzoate. This is the first substrate lacking vicinal hydroxyl groups reported for catecholic extradiol dioxygenases. 2,3-PCD is the final member of the PCA dioxygenase family to be purified. It is compared with other members of this family as well as other catecholic dioxygenases.

Amino Acid Sequence↗