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Lysine 2,3-aminomutase (LAM) catalyzes the interconversion of l-lysine and l-beta-lysine, by a radical mechanism initiated by the reversible, reductive homolytic scission of the C5'-S bond in S-adenosylmethionine (SAM) to form methionine and the 5'-deoxyadenosyl radical at the active site. LAM is a member of a superfamily of enzymes in which a [4Fe-4S]+ cluster with a unique, noncysteinyl coordinated Fe provides the electron required in the cleavage of SAM. Little is known of the mechanism by which the electron is inserted into SAM, and it is not known whether all enzymes of the family employ the same mechanism. Selenium X-ray absorption spectroscopy (XAS) in the reaction of Se-adenosyl-l-selenomethionine (SeSAM) in place of SAM shows that electron transfer occurs by an inner sphere mechanism culminating in direct ligation of selenomethionine to iron upon cleavage of SeSAM. Here, we report an electron nuclear double resonance (ENDOR) spectroscopic investigation of LAM to which has been bound 14N, 17O, 2H, or 13C labeled SAM. It is found that LAM exhibits the same motif for SAM binding to the [4Fe-4S]+,2+ clusters as does pyruvate formate lyase: chelation by the unique iron of the amino and carboxylato groups of SAM; close proximity of the methionine methyl group to the cluster. However, there appear to be significant, and possibly mechanistically important, differences in the details of the binding geometry of SAM. On the basis of the correlation of the ENDOR and XAS spectroscopic results, we postulate a mechanism by which LAM cleaves SAM to generate an intermediate where N, O, and S of the methionine product are bound to the octahedrally coordinated unique Fe of the [4Fe-4S] cluster.

We show the first ENDOR study of the coordination environment of high-spin Co(II) in a biological system with a study of DNA binding to the Co-substituted Cys2/His2 single Zn-finger domain, Finger 3 (F3), from the prototypical zinc finger protein, transcription factor IIIA (TFIIIA) from Xenopus laevis. High covalency to cysteine and histidine is implied by ENDOR-derived 1H couplings to protons of cysteinyl ligands and 14N couplings to histidyl nitrogens, results which support the expectation that Zn(II) and Co(II) bind to F3 in a very similar manner. No changes in either 1H or 14N ENDOR were detected upon binding Co(II)-F3 to C-block DNA. Of particular importance to the use of Co(II) substitution for Zn(II), the ENDOR method shows that Co(II)-F3 undergoes sequence-specific binding to the cognate DNA for Zn(II)-F3, the internal control region (ICR) of the 5S rRNA (C-block). 31P ENDOR measurements yield a Co-31P distance of rCo-P = 8.1(3) A to the nearest backbone phosphodiester of the C-block. Interestingly, a 31P ENDOR doublet observed for Co(II)-F3 in phosphate buffer indicates that inorganic phosphate (Pi) binds at a comparable distance from Co as does the nearest phosphate of DNA, presumably at the same site.

Pyruvate formate-lyase activating enzyme (PFL-AE) generates the catalytically essential glycyl radical on pyruvate formate-lyase via the interaction of the catalytically active [4Fe-4S]+ cluster with S-adenosylmethionine (AdoMet). Like other members of the Fe-S/AdoMet family of enzymes, PFL-AE is thought to function via generation of an AdoMet-derived 5'-deoxyadenosyl radical intermediate; however, the mechanistic steps by which this radical is generated remain to be elucidated. While all of the members of the Fe-S/AdoMet family of enzymes appear to have a unique iron site in the [4Fe-4S] cluster, based on the presence of a conserved three-cysteine cluster binding motif, the role of this unique site has been elusive. Here we utilize 35-GHz pulsed electron nuclear double resonance (ENDOR) studies of the [4Fe-4S]+ cluster of PFL-AE in complex with isotopically labeled AdoMet (denoted [1+/AdoMet]) to show that the unique iron serves to anchor the AdoMet for catalysis. AdoMet labeled with 17O at the carboxylate shows a coupling of A = 12.2 MHz, consistent with direct coordination of the carboxylate to the unique iron of the cluster. This is supported by 13C-ENDOR with the carboxylato carbon labeled with 13C, which shows a hyperfine coupling of 0.71 MHz. AdoMet enriched with 15N at the amino position gives rise to a spectrum with A(15N) = 5.8 MHz, consistent with direct coordination of the amino group to a unique iron of the cluster. Together, the results demonstrate that the unique iron of the [4Fe-4S] cluster anchors AdoMet by forming a classical N/O chelate with the amino and carboxylato groups of the methionine fragment.

Pyruvate formate-lyase activating enzyme (PFL-AE) is a representative member of an emerging family of enzymes that utilize iron-sulfur clusters and S-adenosylmethionine (AdoMet) to initiate radical catalysis. Although these enzymes have diverse functions, evidence is emerging that they operate by a common mechanism in which a [4Fe-4S](+) interacts with AdoMet to generate a 5'-deoxyadenosyl radical intermediate. To date, however, it has been unclear whether the iron-sulfur cluster is a simple electron-transfer center or whether it participates directly in the radical generation chemistry. Here we utilize electron paramagnetic resonance (EPR) and pulsed 35 GHz electron-nuclear double resonance (ENDOR) spectroscopy to address this question. EPR spectroscopy reveals a dramatic effect of AdoMet on the EPR spectrum of the [4Fe-4S](+) of PFL-AE, changing it from rhombic (g = 2.02, 1.94, 1.88) to nearly axial (g = 2.01, 1.88, 1.87). (2)H and (13)C ENDOR spectroscopy was performed on [4Fe-4S](+)-PFL-AE (S = (1)/(2)) in the presence of AdoMet labeled at the methyl position with either (2)H or (13)C (denoted [1+/AdoMet]). The observation of a substantial (2)H coupling of approximately 1 MHz ( approximately 6-7 MHz for (1)H), as well as hyperfine-split signals from the (13)C, manifestly require that AdoMet lie close to the cluster. (2)H and (13)C ENDOR data were also obtained for the interaction of AdoMet with the diamagnetic [4Fe-4S](2+) state of PFL-AE, which is visualized through cryoreduction of the frozen [4Fe-4S](2+)/AdoMet complex to form the reduced state (denoted [2+/AdoMet](red)) trapped in the structure of the oxidized state. (2)H and (13)C ENDOR spectra for [2+/AdoMet](red) are essentially identical to those obtained for the [1+/AdoMet] samples, showing that the cofactor binds in the same geometry to both the 1+ and 2+ states of PFL-AE. Analysis of 2D field-frequency (13)C ENDOR data reveals an isotropic hyperfine contribution, which requires that AdoMet lie in contact with the cluster, weakly interacting with it through an incipient bond/antibond. From the anisotropic hyperfine contributions for the (2)H and (13)C ENDOR, we have estimated the distance from the closest methyl proton of AdoMet to the closest iron of the cluster to be approximately 3.0-3.8 A, while the distance from the methyl carbon to the nearest iron is approximately 4-5 A. We have used this information to construct a model for the interaction of AdoMet with the [4Fe-4S](2+/+) cluster of PFL-AE and have proposed a mechanism for radical generation that is consistent with these results.

EPR (electron paramagnetic resonance) has been used to study interactions of the Ru(III) anticancer compounds imidazolium [trans-RuCl4(1H-imidazole)(DMSO-S)] (NAMI-A) and indazolium [trans-RuCl4(1H-indazole)2] (KP1019) with isolated subcellular components and whole cells of the yeast Saccharomyces cerevisiae. These studies are the first to probe the intracellular speciation of ruthenium using the EPR technique. Initially, NAMI-A and KP1019 were incubated at 30 °C, for time periods up to 24 hours with isolated cell wall, mitochondrial, cytoplasmic, and nuclear fractions of S. cerevisiae. EPR measurements demonstrate that NAMI-A initially forms non-coordinate interactions with each cell component. After longer incubation times these are replaced by coordinated species, particularly with cytoplasmic proteins. KP1019 shows a greater tendency to coordinate directly with cell components, demonstrating significant interactions with mitochondria and cytoplasmic proteins. Subsequently, each complex was incubated with whole cells of S. cerevisiae at 30 °C and whole-cell EPR measurements detected Ru(III) species in measurable concentrations even after 24 hours of incubation. Analysis of the resulting EPR spectra suggests NAMI-A interacts predominantly with cell walls, while KP1019 was found to be coordinating with both the mitochondrial and cytoplasmic protein fractions. Comparison of the signal intensity of these data with those from incubation with whole cells at 4 °C indicates different modes of transmembrane transport for each complex. These studies demonstrate that EPR can provide valuable insight into the oxidation state and speciation of ruthenium compounds in cellular environments.

The behaviour of the antimetastatic Ru(III) complex imidazolium [trans-RuCl₄(1H-imidazole)(DMSO-S)] (NAMI-A) under physiological conditions and its interactions with human serum albumin (hsA) have been studied using electron paramagnetic resonance spectroscopy (EPR). In physiological buffer at pH 7.4, these experiments demonstrate that the DMSO ligand is replaced rapidly by water, and spectra from the subsequent formation of five other Ru(III) complexes show further aquation processes. Although EPR spectra from mono-nuclear Ru(III) complexes are visible after 24 h in buffer, a significant decrease in the overall signal intensity following the first aquation step is consistent with the formation of oxo-bridged Ru(III) oligomers. Incubation with hsA reveals very rapid binding to the protein via hydrophobic interactions. This is followed by coordination through ligand exchange with protein side chains, likely with histidine imidazoles and at least one other specific site. Similar behaviour is observed when the complex is incubated in human serum, indicating that hsA binding dominates speciation in vivo. The addition of ascorbic acid to NAMI-A in buffer leads to quantitative reduction, producing EPR-silent Ru(II) complexes. However, this process is prevented when the complex binds coordinatively to hsA. Together, these results demonstrate the key role that hsA plays in defining the species found in vivo following intravenous treatment with NAMI-A, through prevention of oligomerization and maintenance of the oxidation state, to give protein-bound mono-nuclear Ru(III) species.

To probe the reactivity of ionic liquids relevant to their use in electrochemical applications, the ionic liquid 1-ethyl-3-methylimidazolium tetrachloroaluminate(III) was reacted with metallic lithium to produce a persistent radical, which can be considered a hydrogen-atom adduct of an electron-rich olefin (ERO). Reaction of tetrakis(dimethylamino)ethene, a bona fide ERO, with muonium, produces a structurally similar radical.