X-ray crystal structure of Escherichia coli taurine/alpha-ketoglutarate dioxygenase complexed to ferrous iron and substrates

Taurine/alpha-ketoglutarate dioxygenase (TauD), a non-heme Fe(II) oxygenase, catalyses the conversion of taurine (2-aminoethanesulfonate) to sulfite and aminoacetaldehyde concurrent with the conversion of alpha-ketoglutarate (alphaKG) to succinate and CO(2). The enzyme allows Escherichia coli to use taurine, widely available in the environment, as an alternative sulfur source. Here we describe the X-ray crystal structure of TauD complexed to Fe(II) and both substrates, alphaKG and taurine. The tertiary structure and fold of TauD are similar to those observed in other enzymes from the broad family of Fe(II)/alphaKG-dependent oxygenases, with closest structural similarity to clavaminate synthase. Using the TauD coordinates, a model was determined for the closely related enzyme 2,4-dichlorophenoxyacetate/alphaKG dioxygenase (TfdA), supporting predictions derived from site-directed mutagenesis and other studies of that biodegradative protein. The TauD structure and TfdA model define the metal ligands and the positions of nearby aromatic residues that undergo post-translational modifications involving self-hydroxylation reactions. The substrate binding residues of TauD were identified and those of TfdA predicted. These results, along with sequence alignment information, reveal how TauD selects a tetrahedral substrate anion in preference to the planar carboxylate selected by TfdA, providing insight into the mechanism of enzyme catalysis.     

Substrate-induced conformational changes in Escherichia coli taurine/alpha-ketoglutarate dioxygenase and insight into the oligomeric structure

The enzymes in the alpha-ketoglutarate (alphaKG) dependent dioxygenase superfamily represent the largest class of non-heme iron oxidases and have important medical, ecological, and biotechnological roles. One such enzyme, taurine/alpha-ketoglutarate dioxygenase (TauD), catalyzes the conversion of 2-aminoethanesulfonate (taurine) to sulfite and aminoacetaldehyde while decomposing alphaKG to succinate and CO(2). This alphaKG dependent dioxygenase is expressed in Escherichia coli under sulfur starvation conditions and allows the cell to utilize taurine, and other similar sulfonates in the environment, as an alternative sulfur source. In this work, we report the structures of the apo and holo forms of TauD to 1.9 A resolution (R(cryst) = 21.2%, R(free) = 24.9%) and 2.5 A resolution (R(cryst) = 22.5%, R(free) = 27.8%), respectively. The models reported herein provide significant new insight into the substrate orientations at the active site and the conformational changes that are induced upon taurine binding. Furthermore, analysis of our crystallographic data coupled with reanalysis of the crystallographic model (resolution = 3.0 A, R(cryst) = 28.1, R(free) = 32.0) presented by Elkins et al. (Biochemistry (2002) 41, 5185-5192) reveals an alternative oligomeric arrangement for the enzyme that is consistent with the conserved primary and secondary structure elements of other alphaKG dependent dioxygenases.     

Kinetic dissection of the catalytic mechanism of taurine:alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli

Recent studies on taurine:alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli have provided evidence for a three-step, minimal kinetic mechanism involving the quaternary TauD.Fe(II).alpha-ketoglutarate.taurine complex, the taurine-hydroxylating Fe(IV)-oxo intermediate (J) that forms upon reaction of the quaternary complex with O(2), and a poorly defined, Fe(II)-containing intermediate state that converts in the rate-limiting step back to the quaternary complex [Price, J. C., Barr, E. W., Tirupati, B., Bollinger, J. M., Jr., and Krebs, C. (2003) Biochemistry 42, 7497-7508]. The mapping of this kinetic mechanism onto the consensus chemical mechanism for the Fe(II)- and alpha-ketoglutarate-dependent engendered several predictions and additional questions that have been experimentally addressed in the present study. The results demonstrate (1) that postulated intermediates between the quaternary complex and J accumulate very little or not at all; (2) that decarboxylation of alpha-ketoglutarate occurs prior to or concomitantly with formation of J; (3) that the second intermediate state comprises one or more product complex with Mossbauer features that are partially resolved from those of the binary TauD.Fe(II), ternary TauD.Fe(II).alpha-ketoglutarate, and quaternary TauD.Fe(II).alpha-ketoglutarate.taurine complexes; and (4) that the rate-determining step in the catalytic cycle is release of product(s) prior to the rapid, ordered binding of alpha-ketoglutarate and then taurine to regenerate the O(2)-reactive quaternary complex. The results thus integrate the previously proposed kinetic and chemical mechanisms and indicate which of the postulated intermediates in the latter will be detectable only upon perturbation of the kinetics by changes in reaction conditions (e.g., temperature), protein mutagenesis, the use of substrate analogues, or some combination of these.     

Steady-state and transient kinetic analyses of taurine/alpha-ketoglutarate dioxygenase: effects of oxygen concentration, alternative sulfonates, and active-site variants on the FeIV-oxo intermediate

Taurine/alpha-ketoglutarate (alphaKG) dioxygenase (TauD), an archetype alphaKG-dependent hydroxylase, is a non-heme mononuclear Fe(II) enzyme that couples the oxidative decarboxylation of alphaKG with the conversion of taurine to aminoacetaldehyde and sulfite. The crystal structure of taurine-alphaKG-Fe(II)TauD is known, and spectroscopic studies have kinetically defined the early steps in catalysis and identified a high-spin Fe(IV)-oxo reaction intermediate. The present analysis extends our understanding of TauD catalysis by investigating the steady-state and transient kinetics of wild-type and variant forms of the enzyme with taurine and alternative sulfonates. TauD proteins substituted at residues surrounding the active site were shown to fold properly based on their abilities to form a diagnostic chromophore associated with the anaerobic Fe(II)-alphaKG chelate complex and to generate a tyrosyl radical upon subsequent reaction with oxygen. Steady-state studies of mutant proteins confirmed the importance of His 70 and Arg 270 in binding the sulfonate moiety of taurine and indicated the participation of Asn 95 in recognizing the substrate amine group. The N97A and S158A variants are likely to undergo an increase in hydrophobicity and expansion of the substrate-binding pocket, thus accounting for their decreased K(m) toward pentanesulfonic acid compared to wild-type TauD. Stopped-flow UV-visible spectroscopic examination of the reaction of oxygen with taurine-alphaKG-Fe(II)TauD confirmed a minimal three-step sequence of reactions attributed to Fe(IV)-oxo formation (k(1)), bleaching to the Fe(II) state upon substrate hydroxylation (k(2)), rebinding of excess substrates (k(3)), and indicated that none of the steps exhibit detectable solvent k(H)/k(D) isotope effects. This demonstrates that no protons are involved in the rate-determining step of Fe(IV)-oxo formation, in contrast to heme iron oxygenases. The Fe(IV)-oxo species is likely to be utilized in conversion of the alternative substrates pentanesulfonic acid and 3-N-morpholinopropanesulfonic acid; however, this spectroscopic intermediate was not detected because of the decreased k(1)/k(2) ratio. With taurine, k(1) was shown to depend on the oxygen concentration allowing calculation of a second-order rate constant of 1.58 x 10(5) M(-)(1) s(-)(1) for this irreversible reaction. Stopped-flow analyses of TauD variants provided several insights into how the protein environment influences the rates of Fe(IV)-oxo formation and decay. The Fe(IV)-oxo species was not detected in the N95D or N95A variants because of a reduced k(1)/k(2) ratio, likely related to a decreased substrate-dependent conversion of the six-coordinate to five-coordinate metal site.     

Metal ligand substitution and evidence for quinone formation in taurine/alpha-ketoglutarate dioxygenase

The three metal-binding ligands of the archetype Fe(II)/alpha-ketoglutarate (alphaKG)-dependent hydroxylase, taurine/alphaKG dioxygenase (TauD), were systematically mutated to examine the effects of various ligand substitutions on enzyme activity and metallocenter properties. His99, coplanar with alphaKG and Fe(II), is unalterable in terms of maintaining an active enzyme. Asp101 can be substituted only by a longer carboxylate, with the D101E variant exhibiting 22% the k(cat) and threefold the K(m) of wild-type enzyme. His255, located opposite the O(2)-binding site, is less critical for activity and can be substituted by Gln or even the negatively charged Glu (81% and 33% active, respectively). Transient kinetic studies of the three highly active mutant proteins reveal putative Fe(IV)-oxo intermediates as reported in wild-type enzyme, but with distinct kinetics. Supplementation of the buffer with formate enhances activity of the D101A variant, consistent with partial chemical rescue of the missing metal ligand. Upon binding Fe(II), anaerobic samples of wild-type TauD and the three highly active variants generate a weak green chromophore resembling a catecholate-Fe(III) species. Evidence is presented that the quinone oxidation state of dihydroxyphenylalanine, formed by aberrant self-hydroxylation of a protein side chain of TauD during aerobic bacterial growth, reacts with Fe(II) to form this species. The spectra associated with Fe(II)-TauD and Co(II)-TauD in the presence of alphaKG and taurine were examined for all variants to gain additional insights into perturbations affecting the metallocenter. These studies present the first systematic mutational analysis of metallocenter ligands in an Fe(II)/alphaKG-dependent hydroxylase.     

The first direct characterization of a high-valent iron intermediate in the reaction of an alpha-ketoglutarate-dependent dioxygenase: a high-spin FeIV complex in taurine/alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli

The Fe(II)- and alpha-ketoglutarate(alphaKG)-dependent dioxygenases have roles in synthesis of collagen and sensing of oxygen in mammals, in acquisition of nutrients and synthesis of antibiotics in microbes, and in repair of alkylated DNA in both. A consensus mechanism for these enzymes, involving (i) addition of O(2) to a five-coordinate, (His)(2)(Asp)-facially coordinated Fe(II) center to which alphaKG is also bound via its C-1 carboxylate and ketone oxygen; (ii) attack of the uncoordinated oxygen of the bound O(2) on the ketone carbonyl of alphaKG to form a bicyclic Fe(IV)-peroxyhemiketal complex; (iii) decarboxylation of this complex concomitantly with formation of an oxo-ferryl (Fe(IV)=O(2)(-)) intermediate; and (iv) hydroxylation of the substrate by the Fe(IV)=O(2)(-) complex via a substrate radical intermediate, has repeatedly been proposed, but none of the postulated intermediates occurring after addition of O(2) has ever been detected. In this work, an oxidized Fe intermediate in the reaction of one of these enzymes, taurine/alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli, has been directly demonstrated by rapid kinetic and spectroscopic methods. Characterization of the intermediate and its one-electron-reduced form (obtained by low-temperature gamma-radiolysis of the trapped intermediate) by M?ssbauer and electron paramagnetic resonance spectroscopies establishes that it is a high-spin, formally Fe(IV) complex. Its M?ssbauer isomer shift is, however, significantly greater than those of other known Fe(IV) complexes, suggesting that the iron ligands in the TauD intermediate confer significant Fe(III) character to the high-valent site by strong electron donation. The properties of the complex and previous results on related alphaKG-dependent dioxygenases and other non-heme-Fe(II)-dependent, O(2)-activating enzymes suggest that the TauD intermediate is most probably either the Fe(IV)-peroxyhemiketal complex or the taurine-hydroxylating Fe(IV)=O(2)(-) species. The detection of this intermediate sets the stage for a more detailed dissection of the TauD reaction mechanism than has previously been reported for any other member of this important enzyme family.     

Stopped-flow kinetic studies of the interaction between Escherichia coli Fpg protein and DNA substrates

Formamidopyrimidine-DNA-glycosylase of Escherichia coli (Fpg protein) repairs oxidative DNA damage by removing formamidopyrimidine lesions and 8-oxoguanine residues from DNA. This enzyme possesses three types of activities resulting in the excision of oxidized residue from DNA: hydrolysis of the N-glycosidic bond (DNA glycosylase), beta-elimination (AP-lyase), and delta-elimination. In our work, the kinetic mechanism for 8-oxoguanine excision from DNA substrate with Fpg protein has been determined from stopped-flow measurements of changes in the tryptophan fluorescence. The 12-nucleotide duplex d(CTCTC(oxo)GCCTTCC)*d(GGAAGGCGAGAG) containing the 8-oxoG nucleotide in the sixth position of one strand was used as the specific substrate. Four distinct phases in the time traces were detected. These four-phase transition changes in the Fpg protein fluorescence curves were analyzed by global fitting to determine the intrinsic rate constants. We propose that the first two phases represent the equilibrium steps. The first of them describes the bimolecular binding step and the second, formation of the apurinic site. The third, irreversible step is believed to describe the beta-elimination process. The fourth step reflects the delta-elimination and decomposition of complex between enzyme and the product of 8-oxoG nucleotide excision. The results obtained provide direct evidence of conformational transitions of the Fpg protein during the catalytic process. The significance of these results for the functioning of Fpg protein is discussed.     

Studies with alpha-ketoglutarate dehydrogenase mutants of Escherichia coli

Summary Two classes of mutant lacking -ketoglutarate dehydrogenase complex activity were detected by biochemical analysis of strains of Escherichia coli requiring succinate for aerobic growth on glucose minimal medium. One class, designated sucA, lacked the -ketoglutarate decarboxylase component (E1) whereas the other class, sucB, lacked the dihydrolipoyl transsuccinylase component (E2). Studies with mixed cell-free extracts showed that the overall dehydrogenase activity could be reconstituted from several pairs of sucA plus sucB mutants but not from mixtures of mutants of the same class. Transduction analysis with phage P1 indicated close linkage between the two genes and their frequencies of cotransduction with gal were similar. The order of the two genes was also established as sucA (E1)-sucB(E2)...gal by reciprocal three-point crosses with several pairs of mutants.     

Probing the iron-substrate orientation for taurine/alpha-ketoglutarate dioxygenase using deuterium electron spin echo envelope modulation spectroscopy

The structural relationship between substrate taurine and the non-heme Fe(II) center of taurine/alpha-ketoglutarate (alphaKG) dioxygenase (TauD) was measured using electron spin echo envelope modulation (ESEEM) spectroscopy. Studies were conducted on TauD samples treated with NO, cosubstrate alphaKG, and either protonated or specifically deuterated taurine. Stimulated echo ESEEM data were divided to eliminate interference from 1H and 14N modulations and accentuate modulations from 2H. For taurine that was deuterated at the C1 position (adjacent to the sulfonate group), 2H ESEEM spectra show features that arise from dipole-dipole and deuterium nuclear quadrupole interactions from a single deuteron. Parallel measurements taken for taurine deuterated at both C1 and C2 show an additional ESEEM feature at the deuterium Larmor frequency. Analysis of these data at field positions ranging from g = 4 to g = 2 have allowed us to define the orientation of substrate taurine with respect to the magnetic axes of the Fe(II)-NO, S = 3/2, paramagnetic center. These results are discussed in terms of previous X-ray crystallographic studies and the proposed catalytic mechanism for this family of enzymes.     

Escherichia coli glutamine synthetase adenylyltransferase (ATase, EC 2.7.7.49): kinetic characterization of regulation by PII, PII-UMP, glutamine, and alpha-ketoglutarate

Glutamine synthetase adenylyltranferase (ATase, EC 2.7.7.49) catalyzes the adenylylation and deadenylylation of glutamine synthetase (GS), regulating GS activity. The adenylyltransferase (AT) reaction is activated by glutamine and by the unmodified form of the PII signal transduction protein and is inhibited by the uridylylated form of PII, PII-UMP. Conversely, the adenylyl-removing (AR) reaction is activated by PII-UMP and is inhibited by glutamine and by PII. Both AT and AR reactions are regulated by alpha-ketoglutarate, which binds to PII and PII-UMP. Here, we present a kinetic analysis of the AT and AR activities and their regulation. Both AT and AR reactions used a sequential mechanism of rapid equilibrium random binding of substrates and products. Activators and inhibitors had little effect on the binding of substrates, instead exerting their effects on catalysis. Our results were consistent with PII, PII-UMP, and glutamine shifting the enzyme among at least six different enzyme forms, two of which were inactive, one of which exhibited AR activity, and three of which exhibited AT activity. In addition to a site for glutamine, the enzyme appeared to contain two distinct sites for PII and PII-UMP. The PII, PII-UMP, and glutamine sites were in communication so that the apparent activation and inhibition constants for regulators depended upon each other. The binding of PII was favored by glutamine and its level reduced by PII-UMP, whereas glutamine and PII-UMP competed for the enzyme. alpha-Ketoglutarate, which acts exclusively through its binding to PII and PII-UMP, did not alter the binding of PII or PII-UMP to the enzyme. Rather, alpha-ketoglutarate dramatically affected the extent of activation or inhibition of the enzyme by PII or PII-UMP. A working hypothesis for the regulation of the AT and AR activities, consistent with all data, is presented.     

Deletion analysis of the Escherichia coli taurine and alkanesulfonate transport systems

The Escherichia coli tauABCD and ssuEADCB gene clusters are required for the utilization of taurine and alkanesulfonates as sulfur sources and are expressed only under conditions of sulfate or cysteine starvation. tauD and ssuD encode an alpha-ketoglutarate-dependent taurine dioxygenase and a reduced flavin mononucleotide-dependent alkanesulfonate monooxygenase, respectively. These enzymes are responsible for the desulfonation of taurine and alkanesulfonates. The amino acid sequences of SsuABC and TauABC exhibit similarity to those of components of the ATP-binding cassette transporter superfamily, suggesting that two uptake systems for alkanesulfonates are present in E. coli. Chromosomally located in-frame deletions of the tauABC and ssuABC genes were constructed in E. coli strain EC1250, and the growth properties of the mutants were studied to investigate the requirement for the TauABC and SsuABC proteins for growth on alkanesulfonates as sulfur sources. Complementation analysis of in-frame deletion mutants confirmed that the growth phenotypes obtained were the result of the in-frame deletions constructed. The range of substrates transported by these two uptake systems was largely reflected in the substrate specificities of the TauD and SsuD desulfonation systems. However, certain known substrates of TauD were transported exclusively by the SsuABC system. Mutants in which only formation of hybrid transporters was possible were unable to grow with sulfonates, indicating that the individual components of the two transport systems were not functionally exchangeable. The TauABCD and SsuEADCB systems involved in alkanesulfonate uptake and desulfonation thus are complementary to each other at the levels of both transport and desulfonation.     

Membrane topology model of Escherichia coli alpha-ketoglutarate permease by phoA fusion analysis.

Escherichia coli alpha-ketoglutarate permease (KgtP) is a 432-amino-acid protein that symports alpha-ketoglutarate and protons. KgtP was predicted to contain 12 membrane-spanning domains on the basis of a calculated hydropathy profile. The membrane topology model of KgtP was analyzed by using kgtP-phoA gene fusions and measuring alkaline phosphatase activities in cells expressing the chimeric proteins. Comparisons of the phosphatase activity levels and the locations of the KgtP-PhoA junctions are consistent with the predicted membrane topology model of KgtP.     

A kinetic model of oxygen regulation of cytochrome production in Escherichia coli

Recent experimental work has identified the principal components arrayed by Escherichia coli in its sensing of, and response to, varying levels of oxygen. This apparatus may be leveraged/modified by the metabolic engineer to identify nonuniform oxygen and glucose regimens that deliver better yields than their uniform counterparts. Toward this end we build and analyse a mathematical model that captures the role played by oxygen in the regulation of cytochrome production in E. coli.     

Stopped-flow kinetic analysis of the bacterial luciferase reaction.

The kinetics of the reaction catalyzed by bacterial luciferase have been measured by stopped-flow spectrophotometry at pH 7 and 25 degrees C. Luciferase catalyzes the formation of visible light, FMN, and a carboxylic acid from FMNH2, O2, and the corresponding aldehyde. The time courses for the formation and decay of the various intermediates have been followed by monitoring the absorbance changes at 380 and 445 nm along with the emission of visible light using n-decanal as the alkyl aldehyde. The synthesis of the 4a-hydroperoxyflavin intermediate (FMNOOH) was monitored at 380 nm after various concentrations of luciferase, O2, and FMNH2 were mixed. The second-order rate constant for the formation of FMNOOH from the luciferase-FMNH2 complex was found to be 2.4 x 10(6) M-1 s-1. In the absence of n-decanal, this complex decays to FMN and H2O2 with a rate constant of 0.10 s-1. The enzyme-FMNH2 complex was found to isomerize prior to reaction with oxygen. The production of visible light reaches a maximum intensity within 1 s and then decays exponentially over the next 10 s. The formation of FMN from the intermediate pseudobase (FMNOH) was monitored at 445 nm. This step of the reaction mechanism was inhibited by high levels of n-decanal which indicated that a dead-end luciferase-FMNOH-decanal could form. The time courses for these optical changes have been incorporated into a comprehensive kinetic model. Estimates for 15 individual rate constants have been obtained for this model by numeric simulations of the various time courses.     

Reductive transformation of TNT by Escherichia coli resting cells: kinetic analysis

Microbial 2,4,6-trinitrotoluene (TNT) biotransformation via sequential nitro-reduction appears a ubiquitous process, but the kinetics of these transformations have been poorly understood or described. TNT transformation by Escherichia coli was monitored and a kinetic model for reductive TNT depletion was developed and experimentally calibrated in this report. Using resting cells of aerobically pregrown E. coli, TNT was quickly reduced to hydroxylaminodinitrotoluenes. The standard Michaelis–Menten model was modified to include three additional parameters: product toxicity (T _c), substrate inhibition (K _i), and intracellular reducing power (RH) limitation. Experimentally measured product toxicity (5.2 μmol TNT/mg cellular protein) closely matched the best-fit model value (2.84 μmol TNT/mg cellular protein). Parameter identifiability and reliability (k _m, K _s, T _c, and K _i) was evaluated and confirmed through sensitivity analyses and via Monte Carlo simulations. The resulting kinetic model adequately described TNT reduction kinetics by E. coli resting cells in the absence or presence of reducing power limitation.     

Site-directed mutants of Escherichia coli alpha-ketoglutarate permease (KgtP).

To investigate an active site(s) in the Escherichia coli alpha-ketoglutarate premease, 11 point mutants were made in the corresponding structural gene, kgtP, by oligonucleotide-directed mutagenesis and the polymerase chain reaction. On the basis of sequences conserved in KgtP and related members of a transporter superfamily [Henderson P. J. F., & Maiden, M. C. (1990) Philos. Trans. R. Soc. London B 326, 391], Arg76 was replaced with Ala, Asp, or Lys; Asp88 with Asn or Glu; His90 with Ala; Arg92 with Ala or Lys; and Arg198 with Ala, Asp, or Lys. Mutant proteins expressed using the T7 polymerase system were in each case shown to be membrane-associated. However, they differed in transport activity. Mutants H90A and R198K had activities similar to that of wild type, and R76K and R198A retained 10-60% of the wild-type activity. In all other mutants, alpha-ketoglutarate transport was abolished. The results suggest that Arg92, which is highly conserved among other members of the transporter superfamily, is necessary for activity and also that Asp88 is critical for function, as observed for the tetracycline transporter. These data show further that a positive charge is essential at position 76 and is also important, but not absolutely required, at position 198 for alpha-ketoglutarate transport. Unlike lacY permease which was inactivated by deleting the last helix [McKenna, E., Hardy, D., Pastore, J. C., & Kaback, H. R. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 2969], a KgtP truncation mutant missing the last putative membrane-spanning region was relatively stable and also retained 10-50% of the wild-type level of alpha-ketoglutarate transport activity.     

Stopped-flow spectrophotometric assay of glycerol permeation in Escherichia coli: applicability and limitations.

The passive permeation and facilitated diffusion of glycerol in various strains of Escherichia coli have been studied by stopped-flow spectrophotometry. Contrary to the prediction for glycerol entry by simple diffusion, the reciprocal relaxation time (1/tau, s-1) for the passive permeation of glycerol in cells grown in the presence of glucose was not constant but decreased as the glycerol concentration increased above 100 mM. This anomaly was not due to refractive index differences or to the presence of residual levels of the glycerol facilitator protein in non-induced cells. Although reciprocal relaxation times for glycerol-induced E. coli exhibited the expected elevation relative to non-induced cells, a similar anomalous decrease 1/tar (s-1) with increasing glycerol concentration was observed. In addition, at early times after suspension in dilute buffer, the 1/tau (s-1) values obtained for induced or non-induced E. coli swelling in glycerol were considerably greater than for organisms incubated in dilute buffer for longer times. We concluded that either this spectrophotometric technique was not monitoring solely the permeation of glycerol into E. coli, or concentrations of glycerol above 100 mM significantly perturbed the structure of the E. coli cell envelope.