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Carsten Krebs

Publications and source records attributed to Carsten Krebs.

31 records · Page 2Linked to original sources
PubMed2004

Characterization of the cofactor composition of Escherichia coli biotin synthase.

The cofactor content of in vivo, as-isolated, and reconstituted forms of recombinant Escherichia coli biotin synthase (BioB) has been investigated using the combination of UV-visible absorption, resonance Raman, and Mössbauer spectroscopies along with parallel analytical and activity assays. In contrast to the recent report that E. coli BioB is a pyridoxal phosphate (PLP)-dependent enzyme with intrinsic cysteine desulfurase activity (Ollagnier-deChoudens, S., Mulliez, E., Hewitson, K. S., and Fontecave, M. (2002) Biochemistry 41, 9145-9152), no evidence for PLP binding or for PLP-induced cysteine desulfurase or biotin synthase activity was observed with any of the forms of BioB investigated in this work. The results confirm that BioB contains two distinct Fe-S cluster binding sites. One site accommodates a [2Fe-2S](2+) cluster with partial noncysteinyl ligation that can only be reconstituted in vitro in the presence of O(2). The other site accommodates a [4Fe-4S](2+,+) cluster that binds S-adenosylmethionine (SAM) at a unique Fe site of the [4Fe-4S](2+) cluster and undergoes O(2)-induced degradation via a distinct type of [2Fe-2S](2+) cluster intermediate. In vivo Mössbauer studies show that recombinant BioB in anaerobically grown cells is expressed exclusively in an inactive form containing only the as-isolated [2Fe-2S](2+) cluster and demonstrate that the [2Fe-2S](2+) cluster is not a consequence of overexpressing the recombinant enzyme under aerobic growth conditions. Overall the results clarify the confusion in the literature concerning the Fe-S cluster composition and the in vitro reconstitution and O(2)-induced cluster transformations that are possible for recombinant BioB. In addition, they provide a firm foundation for assessing cluster transformations that occur during turnover and the catalytic competence of the [2Fe-2S](2+) cluster as the immediate S-donor for biotin biosynthesis.

Anaerobiosis↗
PubMed2003

A role for iron in an ancient carbonic anhydrase.

Since 1933, carbonic anhydrase research has focused on enzymes from mammals (alpha class) and plants (beta class); however, two additional classes (gamma and delta) were discovered recently. Cam, from the procaryote Methanosarcina thermophila, is the prototype of the gamma class and the first carbonic anhydrase to be characterized from either an anaerobic organism or the Archaea domain. All of the enzymes characterized from the four classes have been purified aerobically and are reported to contain a catalytic zinc. Herein, we report the anaerobic reconstitution of apo-Cam with Fe2+, which yielded Cam with an effective kcat that exceeded that for the Zn2+-reconstituted enzyme. Mössbauer spectroscopy showed that the Fe2+-reconstituted enzyme contained high spin Fe2+ that, when oxidized to Fe3+, inactivated the enzyme. Reconstitution with Fe3+ was unsuccessful. Reconstitution with Cu2+, Mn2+, Ni2+, or Cd2+ yielded enzymes with effective kcat values that were 10% or less than the value for the Zn2+-reconstituted Cam. Cam produced in Escherichia coli and purified anaerobically contained iron with effective kcat and kcat/Km values exceeding the values for Zn2+-reconstituted Cam. The results identify a previously unrecognized biological function for iron.

Archaea↗
PubMed2003

Structural characterization of the peroxodiiron(III) intermediate generated during oxygen activation by the W48A/D84E variant of ribonucleotide reductase protein R2 from Escherichia coli.

The diiron(II) cluster in the R2 subunit of Escherichia coli ribonucleotide reductase (RNR) activates oxygen to generate a mu-oxodiiron(III) cluster and the stable tyrosyl radical that is critical for the conversion of ribonucleotides to deoxyribonucleotides. Like those in other diiron carboxylate proteins, such as methane monooxygenase (MMO), the R2 diiron cluster is proposed to activate oxygen by formation of a peroxodiiron(III) intermediate followed by an oxidizing high-valent cluster. Substitution of key active site residues results in perturbations of the normal oxygen activation pathway. Variants in which the active site ligand, aspartate (D) 84, is changed to glutamate (E) are capable of accumulating a mu-peroxodiiron(III) complex in the reaction pathway. Using rapid freeze-quench techniques, this intermediate in a double variant, R2-W48A/D84E, was trapped for characterization by Mössbauer and X-ray absorption spectroscopy. These samples contained 70% peroxodiiron(III) intermediate and 30% diferrous R2. An Fe-Fe distance of 2.5 A was found to be associated with the peroxo intermediate. As has been proposed for the structures of the higher valent intermediates in both R2 and MMO, carboxylate shifts to a mu-(eta(1),eta(2)) or a mu-1,1 conformation would most likely be required to accommodate the short 2.5 A Fe-Fe distance. In addition, the diferrous form of the enzyme present in the reacted sample has a longer Fe-Fe distance (3.5 A) than does a sample of anaerobically prepared diferrous R2 (3.4 A). Possible explanations for this difference in detected Fe-Fe distance include an O(2)-induced conformational change prior to covalent chemistry or differing O(2) reactivity among multiple diiron(II) forms of the cluster.

Alanine↗
PubMed2003

Ability of tetrahydrobiopterin analogues to support catalysis by inducible nitric oxide synthase: formation of a pterin radical is required for enzyme activity.

Pterin-free inducible nitric oxide synthase (iNOS) was reconstituted with tetrahydrobiopterin (H(4)B) or tetrahydrobiopterin analogues (5-methyl-H(4)B and 4-amino-H(4)B), and the ability of bound 5-methyl-H(4)B and 4-amino-H(4)B to support catalysis by either full-length iNOS (FLiNOS) or the isolated heme domain (HDiNOS) was examined. In a single turnover with HDiNOS, 5-methyl-H(4)B forms a very stable radical, 5-methyl-H(3)B(*), that accumulates in the arginine reaction to approximately 60% of the HDiNOS concentration and decays approximately 400-fold more slowly than H(3)B(*) (0.0003 vs 0.12 s(-1)). The amount of radical (5-methyl-H(3)B(*) or H(3)B(*)) observed in the NHA reaction is very small (<3% of HDiNOS). The activity of 5-methyl-H(4)B-saturated FLiNOS and HDiNOS is similar to that when H(4)B is bound: arginine is hydroxylated to NHA, and NHA is oxidized exclusively to citrulline and (*)NO. A pterin radical was not observed with 4-amino-H(4)B- or pterin-free HDiNOS with either substrate. The catalytic activity of 4-amino-H(4)B-bound FLiNOS and HDiNOS resembles that of pterin-free iNOS: the hydroxylation of arginine is very unfavorable (<2% that of H(4)B-bound iNOS), and NHA is oxidized to a mixture of amino acid products (citrulline and cyanoornithine) and NO(-) rather than (*)NO. These results demonstrate that the bound pterin cofactor undergoes a one-electron oxidation (to form a pterin radical), which is essential to its ability to support normal NOS turnover. Although binding of H(4)B also stabilizes the NOS structure and active site, the most critical role of the pterin cofactor in NOS appears to be in electron transfer.

Amino Acids↗
PubMed2003

Evidence for hydrogen abstraction from C1 of taurine by the high-spin Fe(IV) intermediate detected during oxygen activation by taurine:alpha-ketoglutarate dioxygenase (TauD).

The Fe(II)- and alpha-ketoglutarate-dependent dioxygenases catalyze hydroxylation reactions of considerable biomedical and environmental significance. Recently, the first oxidized iron intermediate in the reaction of a member of this family, taurine:alpha-ketoglutarate dioxygenase (TauD), was detected and shown to be a high-spin, formally Fe(IV) complex. The demonstration in this study that decay of the Fe(IV) complex is approximately 30-fold slower when it is formed in the presence of 1-[2H]2-taurine provides evidence that the intermediate abstracts hydrogen from C1, the site of hydroxylation, and suggests that quantum-mechanical tunneling may contribute to C1-H cleavage.

Deuterium Exchange Measurement↗
PubMed2003

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 Mössbauer and electron paramagnetic resonance spectroscopies establishes that it is a high-spin, formally Fe(IV) complex. Its Mössbauer 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.

Electron Spin Resonance Spectroscopy↗
PubMed2002

Stoichiometric production of hydrogen peroxide and parallel formation of ferric multimers through decay of the diferric-peroxo complex, the first detectable intermediate in ferritin mineralization.

The catalytic step that initiates formation of the ferric oxy-hydroxide mineral core in the central cavity of H-type ferritin involves rapid oxidation of ferrous ion by molecular oxygen (ferroxidase reaction) at a binuclear site (ferroxidase site) found in each of the 24 subunits. Previous investigators have shown that the first detectable reaction intermediate of the ferroxidase reaction is a diferric-peroxo intermediate, F(peroxo), formed within 25 ms, which then leads to the release of H(2)O(2) and formation of ferric mineral precursors. The stoichiometric relationship between F(peroxo), H(2)O(2), and ferric mineral precursors, crucial to defining the reaction pathway and mechanism, has now been determined. To this end, a horseradish peroxidase-catalyzed spectrophotometric method was used as an assay for H(2)O(2). By rapidly mixing apo M ferritin from frog, Fe(2+), and O(2) and allowing the reaction to proceed for 70 ms when F(peroxo) has reached its maximum accumulation, followed by spraying the reaction mixture into the H(2)O(2) assay solution, we were able to quantitatively determine the amount of H(2)O(2) produced during the decay of F(peroxo). The correlation between the amount of H(2)O(2) released with the amount of F(peroxo) accumulated at 70 ms determined by Mössbauer spectroscopy showed that F(peroxo) decays into H(2)O(2) with a stoichiometry of 1 F(peroxo):H(2)O(2). When the decay of F(peroxo) was monitored by rapid freeze-quench Mössbauer spectroscopy, multiple diferric mu-oxo/mu-hydroxo complexes and small polynuclear ferric clusters were found to form at rate constants identical to the decay rate of F(peroxo). This observed parallel formation of multiple products (H(2)O(2), diferric complexes, and small polynuclear clusters) from the decay of a single precursor (F(peroxo)) provides useful mechanistic insights into ferritin mineralization and demonstrates a flexible ferroxidase site.

Animals↗
PubMed2002

Exchange coupling constant J of peroxodiferric reaction intermediates determined by Mössbauer spectroscopy.

Oxygen activation at a carboxylate-bridged diiron cluster is employed by a number of enzymes for diverse biological functions. The mechanisms by which O(2) is activated at the diferrous clusters have been studied in detail and peroxodiferric reaction intermediates have been observed in several of these diiron proteins. To understand further the magnetic properties of this common reaction intermediate, we have used Mössbauer spectroscopy to determine the magnitude and sign of the exchange coupling constant J (in the exchange Hamiltonian J S(1) x S(2)) of the peroxodiferric intermediates generated during the reactions of O(2) with two different proteins, the recombinant M ferritin from frog and the site-directed variant W48F/D84E of the R2 subunit of ribonucleotide reductase from Escherichia coli. Both intermediates are antiferromagnetically coupled with a moderate coupling constant J of 50+/-10 cm(-1) for R2-W48F/D84E and 75+/-10 cm(-1) for M ferritin. This work demonstrates the capability of Mössbauer spectroscopy to determine exchange coupling constants of diiron complexes, including reaction intermediates. The approach and its limitations are described.

Algorithms↗
PubMed2002

Functional mimic of dioxygen-activating centers in non-heme diiron enzymes: mechanistic implications of paramagnetic intermediates in the reactions between diiron(II) complexes and dioxygen.

Two tetracarboxylate diiron(II) complexes, [Fe(2)(mu-O(2)CAr(Tol))(2)(O(2)CAr(Tol))(2)(C(5)H(5)N)(2)] (1a) and [Fe(2)(mu-O(2)CAr(Tol))(4)(4-(t)BuC(5)H(4)N)(2)] (2a), where Ar(Tol)CO(2)(-) = 2,6-di(p-tolyl)benzoate, react with O(2) in CH(2)Cl(2) at -78 degrees C to afford dark green intermediates 1b (lambda(max) congruent with 660 nm; epsilon = 1600 M(-1) cm(-1)) and 2b (lambda(max) congruent with 670 nm; epsilon = 1700 M(-1) cm(-1)), respectively. Upon warming to room temperature, the solutions turn yellow, ultimately converting to isolable diiron(III) compounds [Fe(2)(mu-OH)(2)(mu-O(2)CAr(Tol))(2)(O(2)CAr(Tol))(2)L(2)] (L = C(5)H(5)N (1c), 4-(t)BuC(5)H(4)N (2c)). EPR and Mössbauer spectroscopic studies revealed the presence of equimolar amounts of valence-delocalized Fe(II)Fe(III) and valence-trapped Fe(III)Fe(IV) species as major components of solution 2b. The spectroscopic and reactivity properties of the Fe(III)Fe(IV) species are similar to those of the intermediate X in the RNR-R2 catalytic cycle. EPR kinetic studies revealed that the processes leading to the formation of these two distinctive paramagnetic components are coupled to one another. A mechanism for this reaction is proposed and compared with those of other synthetic and biological systems, in which electron transfer occurs from a low-valent starting material to putative high-valent dioxygen adduct(s).

Binding Sites↗
PubMed2002

Coordination of adenosylmethionine to a unique iron site of the [4Fe-4S] of pyruvate formate-lyase activating enzyme: a Mössbauer spectroscopic study.

Pyruvate formate-lyase activating enzyme (PFL-AE) generates the catalytically essential glycyl radical of PFL. It is a member of the so-called "radical-SAM superfamily" of enzymes that use a [4Fe-4S] cluster and S-adenosylmethionine (AdoMet or SAM) to catalyze diverse radical-mediated reactions. Evidence suggests that this class of enzymes operate by common initial steps involving the generation of an AdoMet-derived adenosyl radical intermediate, of which the mechanism remains unresolved. The three-cysteine CX3CX2C cluster-binding motif common to all members of this superfamily suggests a unique Fe site in the [4Fe-4S] cluster, which presumably interacts with AdoMet to effect the reductive cleavage and radical generation. Here we employ a dual-iron-isotope (56Fe/57Fe) approach to demonstrate the existence of a unique Fe site in the [4Fe-4S] cluster of PFL-AE by Mössbauer spectroscopy. Coordination of AdoMet to this unique Fe site was made evident by the observation of a substantial increase in the isomer shift (delta) of the Mössbauer spectrum associated with the unique Fe site: delta = 0.42 mm/s in the absence of AdoMet increases to delta = 0.72 mm/s in the presence of AdoMet. Further, the Mössbauer data show that the binding of AdoMet to the unique Fe site occurs in the [4Fe-4S]2+ state, prior to the injection of the reducing equivalent required for catalysis. This observation indicates that AdoMet coordination is a necessary prerequisite to adenosyl radical generation.

Acetyltransferases↗
PubMed2002

Facile electron transfer during formation of cluster X and kinetic competence of X for tyrosyl radical production in protein R2 of ribonucleotide reductase from mouse.

The kinetics and mechanism of formation of the tyrosyl radical and mu-(oxo)diiron(III) cluster in the R2 subunit of ribonucleotide reductase from mouse have been examined by stopped-flow absorption and freeze-quench electron paramagnetic resonance and Mössbauer spectroscopies. The reaction comprises (1) acquisition of Fe(II) ions by the R2 apo protein, (2) activation of dioxygen at the resulting carboxylate-bridged diiron(II) cluster to form oxidized intermediate diiron species, and (3) univalent oxidation of Y177 by one of these intermediates to form the stable radical, with concomitant or subsequent formation of the adjacent mu-(oxo)diiron(III) cluster. The data establish that an oxidized diiron intermediate spectroscopically similar to the well-characterized, formally Fe(III)Fe(IV) cluster X from the reaction of the Escherichia coli R2 protein precedes the Y177 radical in the reaction sequence and is probably the Y177 oxidant. As formation of the X intermediate (1) requires transfer of an "extra" reducing equivalent to the buried diiron cluster following the addition of dioxygen and (2) is observed to be rapid relative to other steps in the reaction, the present data indicate that the transfer of this reducing equivalent is not rate-limiting for Y177 radical formation, in contrast to what was previously proposed (Schmidt, P. P., Rova, U., Katterle, B., Thelander, L., and Gräslund, A. (1998) J. Biol. Chem. 273, 21463-21472). Indeed, the formation of X (k(obs) = 13 +/- 3 s(-1) at 5 degrees C and 0.95 mM O(2)) and the decay of the intermediate to give the Y177 radical (k(obs) = 5 +/- 2 s(-1)) are both considerably faster than the formation of the reactive Fe(II)-R2 complex from the apo protein and Fe(II)(aq) (k(obs) = 0.29 +/- 0.03 s(-1)), which is the slowest step overall. The conclusions that cluster X is an intermediate in Y177 radical formation and that transfer of the reducing equivalent is relatively facile imply that the mouse R2 and E. coli R2 reactions are mechanistically similar.

Amino Acid Substitution↗
PubMed1997

Exchange Coupling in an Isostructural Series of Face-Sharing Bioctahedral Complexes [LM(II)(&mgr;-X)(3)M(II)L]BPh(4) (M = Mn, Fe, Co, Ni, Zn; X = Cl, Br; L = 1,4,7-Trimethyl-1,4,7-triazacyclononane).

The reaction of the divalent metal halides ZnCl(2), ZnBr(2), MnCl(2).4CH(3)CN, MnBr(2), FeCl(2).4CH(3)CN, CoCl(2).4CH(3)CN, CoBr(2), NiCl(2).6H(2)O, and NiBr(2), respectively, with the macrocycle 1,4,7-trimethyl-1,4,7-triazacyclononane (L) (1:1) in anhydrous acetonitrile, acetone, chloroform, or ethanol affords upon additon of NaBPh(4) the isomorphous series of complexes [LM(II)(&mgr;-X)(3)M(II)L]BPh(4): 1, M = Zn, X = Cl; 2, Zn, Br; 3, Mn, Cl; 4, Mn, Br; 5, Fe, Cl; 6, Co, Cl; 7, Co, Br; 8, Ni, Cl; 9, Ni, Br. Six of these complexes have been structurally characterized by single-crystal X-ray crystallography; they crystallize in the triclinic space group P&onemacr; (No. 2) with Z = 4. Crystal data are as follows 1, a = 16.654(1), b = 17.042(1), c = 17.684(1) Å, alpha = 97.30(1), beta = 93.58(1), gamma = 117.46(1) degrees; 3, a = 16.632(8), b = 17.012(8), c = 17.855(5) Å, alpha = 97.16(3), beta = 93.37(3), gamma = 117.24(3) degrees; 5, a = 16.658(3), b = 17.064(3), c = 17.741(4) Å, alpha = 97.32(3), beta = 93.47(3), gamma = 117.36(3) degrees; 6, a = 16.640(3), b = 17.040(3), c = 17.686(4) Å, alpha = 97.39(3), beta = 93.58(3), gamma = 117.39(3) degrees; 8, a = 16.608(3), b = 16.995(3), c = 17.555(3) Å, alpha = 97.36(1), beta = 93.52(1), gamma = 117.52(1) degrees; 9, a = 16.680(3), b = 17.016(2), c = 17.715(3)Å, alpha = 96.99(1), beta = 93.70(1), gamma = 117.42(1) degrees. All complexes consist of a dinuclear, face-sharing bioctahedral monocation with three &mgr;(2)-Cl or &mgr;(2)-Br bridging ligands and two LM fragments and well-separated tetraphenylborate anions (1:1). The cations cocrystallize in two different forms: an enantiomeric form with (lambdalambdalambda) (or (deltadeltadelta)) conformation at both LM fragments and a meso form with an (lambdalambdalambda) conformation at one LM fragment and (deltadeltadelta) at the other (ratio 1:1). From temperature-dependent magnetic susceptibility measurements (2-293 K) it was established that the spins of the unpaired electrons in 3 (d(5)d(5) high spin), 4 (d(5)d(5)), 6 (d(7)d(7) high spin), 7 (d(7)d(7)), 8 (d(8)d(8)), and 9 (d(8)d(8)) are intramolecularly, weakly antiferromagnetically coupled in each case. Surprisingly, the spins order ferromagnetically in 5 (d(6)d(6) high spin). This is in contrast to the previously reported complex [(thf)(3)Fe(II)(&mgr;-Cl)(3)Fe(II)(thf)(3)][SnCl(5)(thf)] (thf = tetrahydrofuran)(5) for which a new analysis of the temperature-dependence of the magnetic susceptibility and of field-dependent Mössbauer spectra establish a weak intramolecular antiferromagnetic coupling. The origin of this difference is analyzed.

Journal Article↗