Acyl and CO Ligands in the [Fe]-Hydrogenase Cofactor Scramble upon Photolysis

[Fe]-hydrogenase harbors the iron-guanylylpyridinol (FeGP) cofactor, in which the Fe(II) complex contains acyl-carbon, pyridinol-nitrogen, cysteine-thiolate and two CO as ligands. Irradiation with UV-A/blue light decomposes the FeGP cofactor to a 6-carboxymethyl-4-guanylyl-2-pyridone (GP) and other components. Previous in vitro biosynthesis experiments indicated that the acyl- and CO-ligands in the FeGP cofactor can scramble, but whether scrambling occurred during biosynthesis or photolysis was unclear. Here, we demonstrate that the [¹⁸O₁-carboxy]-group of GP is incorporated into the FeGP cofactor by in vitro biosynthesis. MS/MS analysis of the ¹⁸O-labeled FeGP cofactor revealed that the produced [¹⁸O₁]-acyl group is not exchanged with a CO ligand of the cofactor, indicating that the acyl and CO ligands are scrambled during photolysis rather than biosynthesis, which ruled out any biosynthesis mechanisms allowing acyl/CO ligands scrambling. Time-resolved infrared spectroscopy indicated that an acyl-Fe(CO)₃ intermediate is formed during photolysis, in which scrambling of the CO and acyl ligands can occur. This finding also suggests that the light-excited FeGP cofactor has a higher affinity for external CO. These results contribute to our understanding of the biosynthesis and photosensitive properties of this unique H₂-activating natural complex.     

Evidence for acyl-iron ligation in the active site of [Fe]-hydrogenase provided by mass spectrometry and infrared spectroscopy

[Fe]-hydrogenase catalyzes the reversible heterolytic cleavage of H(2) and stereo-specific hydride transfer to the substrate methenyltetrahydromethanopterin in methanogenic archaea. This enzyme contains a unique iron guanylylpyridinol (FeGP) cofactor as a prosthetic group. It has recently been proposed-on the basis of crystal structural analyses of the [Fe]-hydrogenase holoenzyme-that the FeGP cofactor contains an acyl-iron ligation, the first one reported in a biological system. We report here that the cofactor can be reversibly extracted with acids; its exact mass has been determined by electrospray ionization Fourier transform ion cyclotron resonance mass-spectrometry. The measured mass of the intact cofactor and its gas-phase fragments are consistent with the proposed structure. The mass of the light decomposition products of the cofactor support the presence of acyl-iron ligation. Attenuated total reflection infrared spectroscopy of the FeGP cofactor revealed a band near wave number 1700 cm(-1), which was assigned to the C=O (double bond) stretching mode of the acyl-iron ligand.     

Carbon monoxide as an intrinsic ligand to iron in the active site of the iron-sulfur-cluster-free hydrogenase H2-forming methylenetetrahydromethanopterin dehydrogenase as revealed by infrared spectroscopy

The iron-sulfur-cluster-free hydrogenase Hmd (H(2)-forming methylenetetrahydromethanopterin dehydrogenase) from methanogenic archaea has recently been found to contain one iron associated tightly with an extractable cofactor of yet unknown structure. We report here that Hmd contains intrinsic CO bound to the Fe. Chemical analysis of Hmd revealed the presence of 2.4 +/- 0.2 mol of CO/mol of iron. Fourier transform infrared spectra of the native enzyme showed two bands of almost equal intensity at 2011 and 1944 cm(-)(1), interpreted as the stretching frequencies of two CO molecules bound to the same iron in an angle of 90 degrees . We also report on the effect of extrinsic (12)CO, (13)CO, (12)CN(-), and (13)CN(-) on the IR spectrum of Hmd.     

The Bacterial [Fe]‐Hydrogenase Paralog HmdII Uses Tetrahydrofolate Derivatives as Substrates

[Fe]‐hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyl‐tetrahydromethanopterin (methenyl‐H₄MPT⁺) with H₂. H₄MPT is a C1‐carrier of methanogenic archaea. One bacterial genus, Desulfurobacterium, contains putative genes for the Hmd paralog, termed HmdII, and the HcgA–G proteins. The latter are required for the biosynthesis of the prosthetic group of Hmd, the iron–guanylylpyridinol (FeGP) cofactor. This finding is intriguing because Hmd and HmdII strictly use H₄MPT derivatives that are absent in most bacteria. We identified the presence of the FeGP cofactor in D. thermolithotrophum. The bacterial HmdII reconstituted with the FeGP cofactor catalyzed the hydrogenation of derivatives of tetrahydrofolate, the bacterial C1‐carrier, albeit with low enzymatic activities. The crystal structures show how Hmd recognizes tetrahydrofolate derivatives. These findings have an impact on future biotechnology by identifying a bacterial Hmd paralog.     

Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H2 Binding Site in Open and Closed Protein Conformations

A series of QM/MM optimizations of the full protein of [Fe] hydrogenase were performed. The FeGP cofactor has been optimized in the water‐bound resting state ( 1 ), with a side‐on bound dihydrogen ( 2 ), or as a hydride intermediate ( 3 ). For inclusion of H₄ MPT in the closed structure, advanced multiscale modeling appears to be necessary, especially to obtain reliable distances between CH‐H₄MPT⁺ and the dihydrogen (H₂) or hydride (H^?) ligand in the FeGP cofactor. Inclusion of the full protein is further important for the relative energies of the two intermediates 2 and 3 . We finally find that hydride transfer from 3 has a significantly higher barrier than found in previous studies neglecting the full protein environment.     

Mössbauer studies of the iron-sulfur cluster-free hydrogenase: the electronic state of the mononuclear Fe active site

The iron-sulfur cluster-free hydrogenase (Hmd) from methanogenic archaea harbors an iron-containing, light-sensitive cofactor of still unknown structure as prosthetic group. The enzyme is reversibly inhibited by CO and cyanide and is EPR silent. We report here on M?ssbauer spectra of the (57)Fe-labeled enzyme and of the isolated cofactor. The spectrum of the holoenzyme measured at 80 K revealed a doublet peak with an isomer shift delta = 0.06 mm.s(-)(1) and a quadrupole splitting of DeltaE(Q) = 0.65 mm.s(-)(1) (at pH 8.0). The signal intensity corresponded to the enzyme concentration assuming 1 Fe per mol active site. Upon addition of CO or cyanide to the enzyme, the isomer shift decreased to -0.03 mm.s(-)(1) and -0.00(1) mm.s(-)(1), and the quadrupole splitting increased to 1.38 mm.s(-)(1) and 1.75 mm.s(-)(1), respectively. The three spectra could be perfectly simulated assuming the presence of only one type of iron in Hmd. The low isomer shift is characteristic for Fe in a low oxidation state (0, +1, +2). When the spectra of the holoenzyme and of the CO- or cyanide-inhibited enzyme were measured at 4 K in a magnetic field of 4 and 7 T, the spectra obtained could be simulated assuming the presence of only the external magnetic field, which excludes that the iron in the active site of Hmd is Fe(I), high-spin Fe(0), or high-spin Fe(II). M?ssbauer spectra of the isolated Hmd cofactor are also reported.     

Electron-transfer chemistry of the iron-molybdenum cofactor of nitrogenase: delocalized and localized reduced states of FeMoco which allow binding of carbon monoxide to iron and molybdenum

The electron-transfer chemistry of the isolated iron-molybdenum cofactor of nitrogenase (FeMoco) has been studied by electrochemical and spectroelectrochemical methods. Two interconverting forms of the cofactor arise from a redox-linked ligand isomerism at the terminal iron atom; this is attributed to rotamerism of an anionic N-methyl formamide ligand bound at this site. FeMoco in its EPR-silent oxidised state is shown to undergo three successive one-electron transfer steps. We argue that the first and second redox processes are associated with electron-transfer delocalised over the iron-sulfur core of the cofactor, whilst the third irreversible process is localised on molybdenum. This is strongly reinforced by spectroelectrochemical studies under (12)CO and (13)CO which reveal two independent carbon monoxide binding sites that are specifically associated with the second (iron core) and third (molybdenum) electron-transfer processes and which give rise to terminal nu((12)CO) bands at 1885 and 1920 cm(-1) respectively. Moreover, in parallel with earlier studies on the enzyme system, it is shown that at low CO concentration, carbon monoxide binds to the cofactor in bridging modes, with nu(CO) bands at 1835 and 1808 cm(-1) that are interconverted by single-electron transfer. Importantly we show that the contentious overall 2e difference in the assignment of the metal oxidation levels in the resting state of the enzyme-bound cofactor, arising from analysis of (57)Fe ENDOR and M?ssbauer data, can be resolved in the light of the electron-transfer chemistry of the isolated cofactor described herein.     

Biosynthetic study of amphidinolide W

The biosynthetic origins of amphidinolide W (1) were investigated on the basis of (13)C-NMR data of 13C-enriched samples obtained by feeding experiments with [1-13C], [2-13C], and [1,2-13C2] sodium acetate in cultures of a strain Y-42 of the dinoflagellate Amphidinium sp. These incorporation patterns suggested that 1 was generated from a hexaketide chain, two acetate units, four isolated C1 units from C-2 of acetates, and four branched C1 units from C-2 of acetates. The acetate-incorporation patterns for C-1-C-2-(C-21) and C-8-C-18-(C-23, C-24) of 1 corresponded well to those for C-1-C-2-(C-27) and C-5-C-15-(C-28, C-29) of amphidinolide H (2) isolated from this strain.     

Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm(-1), consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at approximately 311 cm(-1) and another reproducible feature at approximately 380 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.     

Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics

Methanogenesis, the anaerobic production of methane from CO2 or simple carbon compounds, requires seven organic coenzymes. This review describes pathways for the biosynthesis of methanofuran, 5,6,7,8-tetrahydromethanopterin, coenzyme F420, coenzyme M (2-mercaptoethanesulfonic acid) and coenzyme B (7-mercaptoheptanoyl-L-threonine phosphate). Spectroscopic evidence for the pathways is reviewed and recent efforts are described to identify and characterize the biosynthetic enzymes from methanogenic archaea. The literature from 1971 to September 2001 is reviewed, and 169 references are cited.     

丁撑桥联蝶状铁硫原子簇配合物[(μ-ZS)Fe2(CO)6[μ-S(CH2)4-S-μ[(μ-ZS)Fe2(CO)6]的合成结构及构象

双Grignard试剂BrMg(CH2)4MgBr可还原断裂两分子μ-S2Fe2(CO)6的硫-硫键,生成丁撑桥联双簇铁硫中间物A, [(μ-BrMgS)Fe2(CO)6]μ-S(CH2)4S-μ-[(μ-BrMgS)Fe2(CO)6], A于原位(in situ)进一步同卤代烃、氯甲醚、氯代酮、氯代酯或酰氯作用, 共得到10个结构新颖的丁撑桥联双簇铁硫配合物B, [(μ-ZS(Fe2(CO)6]μ-S(CH2)4S-μ[(μ-ZS)Fe2(CO)6]. 除通过IR、^1H NMR及碳氢分析证实上述配合物的结构和推得某些配合物可能的构象外, 还用X衍射法确证了其中一个配合物B(1)的结构和构象.     

Electron inventory, kinetic assignment (E(n)), structure, and bonding of nitrogenase turnover intermediates with C2H2 and CO

Improved 1H ENDOR data from the S(EPR1) intermediate formed during turnover of the nitrogenase alpha-195Gln MoFe protein with C2(1,2)H2 in (1,2)H2O buffers, taken in context with the recent study of the intermediate formed from propargyl alcohol, indicate that S(EPR1) is a product complex, likely with C2H4 bound as a ferracycle to a single Fe of the FeMo-cofactor active site. 35 GHz CW and Mims pulsed 57Fe ENDOR of 57Fe-enriched S(EPR1) cofactor indicates that it exhibits the same valencies as those of the CO-bound cofactor of the lo-CO intermediate formed during turnover with CO, [Mo4+, Fe3+, Fe6(2+), S9(2-)(d43)](+1), reduced by m = 2 electrons relative to the resting-state cofactor. Consideration of 57Fe hyperfine coupling in S(EPR1) and lo-CO leads to a picture in which CO bridges two Fe of lo-CO, while the C2H4 of S(EPR1) binds to one of these. To correlate these and other intermediates with Lowe-Thorneley (LT) kinetic schemes for substrate reduction, we introduce the concept of an "electron inventory". It partitions the number of electrons a MoFe protein intermediate has accepted from the Fe protein (n) into the number transmitted to the substrate (s), the number that remain on the intermediate cofactor (m), and the additional number delivered to the cofactor from the P clusters (p): n = m + s - p (with p = 0 here). The cofactors of lo-CO and S(EPR1) both are reduced by m = 2 electrons, but the intermediates are not at the same LT reduction stage (E(n)): (n = 2; m = 2, s = 0) for lo-CO; (n = 4; s = 2, m = 2) for S(EPR1). This is the first proposed correlation of an LT E(n) kinetic state with a well-defined chemical state of the enzyme.     

The source of the carbon monoxide in the classical Belousov-Zhabotinsky reaction

CO and CO2 evolution was measured in a cerium and in a ferroin-catalyzed Belousov-Zhabotinsky (BZ) reaction. These gases were stripped from the reaction mixture by a N2 carrier gas, mixed with H2, converted to methane on a Ni catalyst, and then measured by a flame ionization detector (FID). CO could be detected separately by absorbing CO2 on a soda lime column. In separate experiments it was proven that CO is produced in a reaction of BrO2* radicals with bromomalonic acid (BrMA). To this end BrO2(.-) radicals were generated in two different ways: (i) in the reaction HBrO2 + HBrO3 <--> 2 BrO2(.-) + H2O and (ii) by reducing HBrO3 to BrO2(.-) by Fe(2+). It was found that (.-)OH radicals--produced by Fenton's reagent--can also generate CO from BrMA. We propose that CO can be formed when an inorganic radical (like BrO2(.-) or (.-)OH) reacts with the enol form of BrMA producing an acyl radical which decarbonylates in the next step. Malonic acid (MA)-BrMA mixtures were prepared by a new method modifying Zaikin and Zhabotinsky's original recipe to minimize the production of dibromomalonic acid (Br2MA).     

Calculated vibrational frequencies for FeMo-co, the active site of nitrogenase, bearing hydrogen atoms and carbon monoxide

The intramolecular hydrogenation paradigm for the reducing actions of the enzyme nitrogenase postulates that the iron-molybdenum cofactor (FeMo-co, Fe(7)MoS(9)N(homocitrate)) as active site contains H atoms bound to Fe and S during the catalytic cycle, and that these H atoms are the reducing agents. The reduction of N(2) and of all other non-physiological substrates is strongly inhibited by carbon monoxide, except for the formation of H(2) from protons. It has been recently reported that vanadium nitrogenase and modified molybdenum nitrogenase reduce CO to hydrocarbons. Therefore many questions now arise about relationships between CO and H on the nitrogenase cofactors. In order to assist the interpretation of kinetic infrared spectral data, vibrational frequencies and modes have been calculated for a variety of possible structures in which FeMo-co bears H atoms, or CO ligands, or both. Fe-H stretching frequencies occur in the same spectral window as the C-O stretching frequencies, with lesser intensity, and both stretches are strongly coupled in some structures. Symmetrical bridging of CO between two Fe atoms of FeMo-co is destabilised by the presence of other ligands on Fe, and the reason for this is evident. Two results for bound formyl, HCO, are reported. These calculations of reference structures allow some interpretation of existing experimental spectra, but, more significantly, they suggest further kinetic infrared experiments to elucidate the chemical mechanism of catalysis by nitrogenase under normal turnover conditions.     

醋酸乙烯酯基桥连铁硫配合物(σ,π-μ-CH3CO2C=CH2)(μ-RS)Fe2CO)6的制备及结构鉴定

本文报道乙酰氯同[μ-CO)(μ-RS)Fe2(CO]Et3NH相作用生成了标题化合物, 除用碳氢分析, IR, 'HNMR及X衍射技术表征这类配合物的结构和构象外, 还对形成此类产物的过程进行了初步讨论。     

Collision-induced dissociation of uracil and its derivatives

The collision-induced dissociation of protonated uracil has been studied by tandem mass spectrometry using models extensively labeled with stable isotopes, and derivatives of the kinds found in nucleic acids. Following collisional activation at 30 eV translational energy, protonated uracil dissociates through two principal pathways which do not occur in electron ionization mass spectra: (1) elimination of NH3 almost entirely from N-3, followed by loss of CO from C-4, 0⁴; (2) loss of H2O, equally from 0² and 0⁴. Elimination of HNCO, also the principal dissociation process from odd-electron molecular ions, proceeds primarily by loss of N-3, C-Z, O² and 10% from N-l, C-Z, 0². Several secondary dissociation products are formed with quantitative site specificity of skeletal atoms: C,HO+ (4-C0, C-5, C-6); H2CN+ (N-l, C-6); C2H2+ (N-l, C-5, C-6). First-step dissociation reactions are interpreted in terms of pyrimidine ring opening at likely sites of protonation after collisional activation of MH+. Collision-induced dissociation mass spectra of uracils with structural themes common to nucleic acids (methylation, replacement of 0 by S, C-5 substitution) follow analogous reaction paths which permit assignment of sites of substitution, and exhibit ion abundance changes attributed to differences in substituent basicity and electron density.     

Characterization of acylphosphatidylglycerols from <Emphasis Type="Italic">salmonella typhimurium</Emphasis> by tandem mass spectrometry with electrospray ionization

Acylphosphatidylglycerol (Acyl-PG), a polar lipid class containing three fatty acyl groups, was isolated from Salmonella bacteria and characterized by tandem quadrupole and quadrupole ion-trap mass spectrometric methods with electrospray ionization. The structural characterization of the acyl-PG with various acyl groups (A-B/C-PG, where A not equal B not equal C) is based on the findings that the carboxylate anions (R(x)CO(2)(-)) arising from sn-2 (R(2)CO(2)(-)) is more abundant than that arising from sn-3' (R(3')CO(2)(-)), which is much more abundant than that arising from sn-1 (R(1)CO(2)(-)). This information provides a simple method for determination of the fatty acyl moieties and their positions in the molecule. The structural identification of the molecule can also be achieved by the findings that the fragment ion reflecting the ketene loss at sn-2 is more prominent than that reflecting the acid loss (i.e., [M - H - R'(2)CH=CO](-) > [M - H - R(2)CO(2)H](-)), while the ion arising from acid loss at sn-1 or sn-3' is, respectively, more abundant than the corresponding ketene loss (i.e., [M - H - R(1)CO(2)H](-) > [M - H - R'(1)CH=CO](-); [M - H - R(3')CO(2)H](-) > [M - H -R'(3')CH=CO](-)). The identity of the acyl moiety at sn-3' can be confirmed by an acyl-glycerophosphate anion observed in the product-ion spectrum obtained with a triple-stage quadrupole (TSQ) instrument, but not in that obtained with an ion-trap mass spectrometer (ITMS). However, the MS(2)-spectrum obtained with an ITMS is featured by the ion series that abundances of [M - H - R'(2)CH=CO - R(3)CO(2)H - 74](-) > [M - H - R'(2)CH=CO - R(1)CO(2)H - 74](-) z.Gt; [M - H - R'(1(or 3'))CH=CO - R(3'(or 1))CO(2)H - 74](-). This information also facilitates structural elucidation of the acyl-PG subclass that contains various acyl substituents. Structural identifications of molecular species having two identical fatty acyl substituents at sn-1, sn-2, or sn-3' or consisting of more than one isomeric structures are also demonstrated. The identities of the minor isomeric species in the molecules can be revealed by the aforementioned structural information arising from the various ion series combined.     

Identification of HcgC as a SAM‐Dependent Pyridinol Methyltransferase in [Fe]‐Hydrogenase Cofactor Biosynthesis

Previous retrosynthetic and isotope‐labeling studies have indicated that biosynthesis of the iron guanylylpyridinol (FeGP) cofactor of [Fe]‐hydrogenase requires a methyltransferase. This hypothetical enzyme covalently attaches the methyl group at the 3‐position of the pyridinol ring. We describe the identification of HcgC, a gene product of the hcgA‐G cluster responsible for FeGP cofactor biosynthesis. It acts as an S‐adenosylmethionine (SAM)‐dependent methyltransferase, based on the crystal structures of HcgC and the HcgC/SAM and HcgC/S‐adenosylhomocysteine (SAH) complexes. The pyridinol substrate, 6‐carboxymethyl‐5‐methyl‐4‐hydroxy‐2‐pyridinol, was predicted based on properties of the conserved binding pocket and substrate docking simulations. For verification, the assumed substrate was synthesized and used in a kinetic assay. Mass spectrometry and NMR analysis revealed 6‐carboxymethyl‐3,5‐dimethyl‐4‐hydroxy‐2‐pyridinol as the reaction product, which confirmed the function of HcgC.     

A Water‐Bridged H‐Bonding Network Contributes to the Catalysis of the SAM‐Dependent C‐Methyltransferase HcgC

[Fe]‐hydrogenase hosts an iron‐guanylylpyridinol (FeGP) cofactor. The FeGP cofactor contains a pyridinol ring substituted with GMP, two methyl groups, and an acylmethyl group. HcgC, an enzyme involved in FeGP biosynthesis, catalyzes methyl transfer from S ‐adenosylmethionine (SAM) to C3 of 6‐carboxymethyl‐5‐methyl‐4‐hydroxy‐2‐pyridinol ( 2 ). We report on the ternary structure of HcgC/S ‐adenosylhomocysteine (SAH, the demethylated product of SAM) and 2 at 1.7 Å resolution. The proximity of C3 of substrate 2 and the S atom of SAH indicates a catalytically productive geometry. The hydroxy and carboxy groups of substrate 2 are hydrogen‐bonded with I115 and T179, as well as through a series of water molecules linked with polar and a few protonatable groups. These interactions stabilize the deprotonated state of the hydroxy groups and a keto form of substrate 2 , through which the nucleophilicity of C3 is increased by resonance effects. Complemented by mutational analysis, a structure‐based catalytic mechanism was proposed.     

Efficient methods for the synthesis of 2-hydroxyphenazine based on the Pd-catalyzed N-arylation of aryl bromides

[reaction: see text] Substituted diphenylamines can be synthesized by Pd(0)-catalyzed N-arylation using o-nitroanilines and nitro-substituted aryl bromides for a substrate. Cyclization of the diphenylamines by various methods, including the intramolecular Pd(0)-catalyzed N-arylation, produces 2-methoxyphenazine which can easily be deprotected to give 2-hydroxyphenazine. This phenazine is required to synthesize methanophenazine, a novel redoxactive cofactor isolated from methanogenic archaea.