Structural heterogeneity and purification of protein-free F430 from the cytoplasm of Methanobacterium thermoautotrophicum

F430 is the nickel containing tetrapyrrole cofactor of S-methyl coenzyme M methylreductase, the enzyme that catalyzes the final step of methane production by methanogenic bacteria: the reduction of S-methyl coenzyme M (H3CSCH2CH2SO3-) to methane and coenzyme M (HSCH2CH2SO3-). The protein-free F430 obtained from the cytosol of Methanobacterium thermoautotrophicum, strain delta H, exists predominantly in two isomeric forms that differ in relative stereochemical disposition of acid side chains at the 12 and 13 positions of the macrocycle periphery (Pfaltz, A., Livingston, D. A., Jaun, B., Diekert, G., Thauer, R. K., and Eschenmoser, A. (1985) Helv. Chim. Acta 68, 1338-1358). A simple one-step chromatographic procedure for the large-scale separation of these isomers is described. X-ray absorption spectroscopic studies show that F430 (i.e. the native isomer) is 6-coordinate with long nickel-ligand bonds (approximately 2.1 A), suggesting an approximately planar macrocycle. In contrast, the 12,13-diepimer exhibits a 4-coordinate, square-planar structure with short nickel-nitrogen bonds (approximately 1.9 A), suggesting a ruffled macrocycle. Previous reports, based on other x-ray absorption spectroscopic data, of static disorder in F430 Ni-N distances are shown to be incorrect due to sample heterogeneity. The optical spectrum of F430 (whether purified from the protein-free cytosol or extracted at high ionic strength from the holoenzyme) differs significantly from that of the 12,13-diepimer. The optical spectral differences are correlated with the alterations in coordination number and geometry of the central nickel ion in the two F430 isomers.     

Functional relationship between protein-bound and free factor F430 in Methanobacterium

Factor F430 is a nickel porphinoid present in all methanogenic bacteria. It is a component of methyl-CoM reductase to which it is tightly but not covalently bound. Evidence is presented that in Methanobacterium thermoautotrophicum grown on nickel sufficient medium only approximately 30% of total F430 is associated with methyl-CoM reductase and that 70% is present in a non-bound, free form. When such cells were transferred to a nickel deficient medium the bacteria continued to grow although synthesis of total F430 stopped. During growth in the absence of nickel the amount of total F430 per 1 culture remained constant and that per g cells decreased. The ratio of free F430 to bound F430, however, changed. Free F430 was converted into the protein-bound form until almost all of the free F430 had disappeared. The kinetics of labelling with ⁶³Ni of free and bound F430 agreed rather well with that calculated for a precursor-product relationship between free and bound F430.Dedicated to Professor H. G. Schlegel on the occasion of his 60th birthday     

Structural and spectroscopic characterization of exogenous ligand binding to isolated factor F430 and its configurational isomers

Binding of axial ligands to the nickel(II) of isolated factor F430 from the methyl reductase enzyme of Methanobacterium thermoautotrophicum is demonstrated. Evidence of bis-ligand coordination is obtained from the x-ray absorption, optical, and resonance Raman spectral characterization of F430 and its 12,13-diepimeric isomer in the presence of a large excess of cyanide, pyridine, or 1-methylimidazole. Significant broadening and 5-10-nm red shifts of the main 430-nm optical absorption band and shifts of up to 30 cm-1 for the high-frequency Raman lines are observed upon coordination of these axial ligands. The Raman spectra of native F430 and the diepimer with a particular axial ligand are nearly identical. Nickel x-ray absorption edge spectra of the diepimer in the absence and presence of these exogenous ligands are indicative of conversion from a square-planar to a tetragonally distorted octahedral geometry. Analyses of the nickel extended x-ray absorption fine structure data for the ligated diepimer complexes yield detailed structural information for these complexes. Implications of these data with respect to the enzymatic mechanism and the structure of the enzyme-bound factor are discussed.     

Modeling Study on the Cleavage Step of the Self-Splicing Reaction in Group I Introns

Abstract

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E.J. Mol. Biol. 216, 585–610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of PI helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A M., Murphy, F. L., Cech, T. R. Nature 358, 123–128. (1992)), based on mutational studies involving the J8/7 segment Two hydrated Mg²⁺ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25–33 (1991)) as a guide. Thepresence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg²⁺ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg²⁺ complexes in catalysis is further explored using molecular orbital calculations.     

Complexes formed from 2,4,6-trimercaptotriazine (H3TMT): synthesis and structural characterization of [M(PhP(CH2CH2P(Ph)2)2(HTMT)], M=Ni(II), Pd(II), Pt(II)

Na₃TMT · 9H₂O (H₃TMT=2,4,6-trimercaptotriazine) reacts with M(PPP)Cl₂, PPP=PhP(CH₂CH₂PPh₂)₂, M=Ni, Pd, Pt, to give the compounds [M(PPP)(HTMT)]. The nickel and palladium complexes have been characterized by single-crystal X-ray diffraction analysis. PPP is tridentate in both complexes. The nickel complex has an irregular trigonal bipyramidal configuration in which the triazine is bidentate, coordinating through one sulfur and one nitrogen donor atom. The palladium complex has an approximately square planar geometry in which the triazine forms a strong Pd-S bond in the plane and also a very weak Pd-N interaction above the plane. The ³¹P NMR spectrum of the platinum complex is similar to that of the palladium complex, which is consistent with the Pt complex also having an approximately square-planar structure. Variable temperature NMR spectra show that two conformational isomers of the nickel complex are present in solution at low temperatures, though exchange is fast at room temperature. DFT calculations have confirmed the possible existence of two five-coordinate isomers of comparable stability.     

Structural diversity in five-coordinate nickel(II) complexes of the tripyrrin ligand

Three different five coordinate nickel(II) complexes of tripyrrin ligands with chloro, oxalato and nitrato anionic ligands were obtained by ligand exchange reactions from respective trifluoroacetato species prepared in situ. Crystallographic studies of these compounds revealed different coordination geometries as well as different packing pattern. In the solid, the chloride complex accepts one water ligand to form a distorted trigonal bipyramid with two N donor centers in apical and one in an equatorial position. The molecules are organized in the crystal via hydrogen bonds, resulting in endless chains. Oxalate serves as a bridging ligand between two nickel(II) tripyrrins. Again the coordination of nickel(II) is found to be trigonal bipyramidal but with two equatorial and one apical nitrogen donors. The discrete dinuclear complexes are arranged in the crystal in a way as to form channels filled with toluene molecules. The nitrate species displays a η² bound nitrate ligand and short contacts between the nickel(II) center and an ethyl substituent of a neighboring molecule. The complex shows an unusually distorted molecular structure and unexpected differences in the two Ni-O bond lengths.     

Coordination chemistry of F430. Axial ligation equilibrium between square-planar and bis-aquo species in aqueous solution

X-ray absorption spectroscopic characterization of axial ligand coordination to factor F430, the nickel-tetrapyrrole cofactor of the S-methyl-coenzyme M (CH3SCoM) methyl reductase enzyme from methanogenic bacteria, is presented. The nickel of isolated F430 is hexacoordinate at 10 K in aqueous solution (as is the enzyme-bound cofactor), whereas the epimerized and ring-oxidized derivatives of F430 have four-coordinate nickel. Reduction of the ring-oxidized derivative, F560, with dithionite yields F430 in its native configuration, with axial ligands indistinguishable from those present when the cofactor is obtained directly from the holoenzyme. Thus, we conclude that the axial ligands to F430 in aqueous solution are water molecules. Analysis of the nickel extended x-ray absorption fine structure is consistent with this conclusion. Resonance Raman spectra obtained at room temperature contain features characteristic of both 4- and 6-coordinate forms of the cofactor. We have found that the resonance Raman, optical, and x-ray absorption spectra of aqueous solutions of F430 are temperature-dependent due to a ligand-binding equilibrium involving the square-planar and 6-coordinate bis-aquo forms of the cofactor. At low temperatures (less than 250 K) the 6-coordinate form predominates, whereas higher temperature solutions contain both 4- and 6-coordinate species in a dynamic equilibrium. Similar behavior is observed in other weakly coordinating solvents such as methanol and ethanol. The 4-coordinate form is predominant in solvents with strong electron-withdrawing substituents such as 2,2,2-trifluoroethanol and 2-mercaptoethanol. The relevance of this facile ligand exchange to the active site structure and enzymatic mechanism of the parent enzyme is discussed.     

GlcNAc-Thiazoline conformations

The title compound, a powerful inhibitor of retaining N-acetylhexosaminidases, can move freely among three pyranose solution conformations of similar energy—two twist boats and the ⁴C₁ chair—as revealed by NMR, calculational, and crystallographic studies. It binds in the enzyme active site only in the pseudo-⁴C₁ conformation, however, in which it most closely resembles the hypothetical bound substrate transition state, a ⁴E sofa that is approximately trigonal bipyramidal at the anomeric carbon.     

Copper(II), cobalt(II) and nickel(II) complexes of alkyl-substituted tris(2-benzimidazolylmethyl)amines and their ternary copper(II) systems containing several thiolates

Copper(II), cobalt and nickel(II) complexes of tris(benzimidazolylmethyl)amine(1) and of its methyl(2), isobutyl(3) or isopropyl(4)-substituted derivatives of one of the backbone methylene groups were prepared and characterized. The ligands (1)–(3) afforded trigonal bipyramidal copper(II) complexes, whereas ligand (4) gave a tetrahedrally distorted tetragonal one because of the steric hindrance arising from the isopropyl group. All the cobalt(II) complexes prepared were supposed to be tetrahedral or pseudotrigonal bipyramidal, and all the nickel(II) complexes to be slightly tetrahedrally distorted octahedral. Ternary copper(II) systems containing several thiolates as the third component exhibited intense blue, brown or green color under a reduced temperature by virtue of the charge transfer bands, S^? → Cu.     

Five-coordinated rhodium(I) carbonyl compounds

The title compounds were synthesised by the replacement of chlorine in Rh(CO)(PPh₃)₂Cl with monobasic bidentate chelating ligands such as salicylaldehyde, acetylacetone, benzoylacetone, dibenzoylmethane, 8-hydroxyquinoline, benzoylphenyl hydroxylamine, 2-hydroxyacetophenone and 2-hydroxybenzophenone. IR spectral evidence points out that these compounds have a trigonal bipyramidal geometry around rhodium in the solid state. However, in benzene solutions, except for the 8-hydroxyquinoline and 2-hydroxybenzophenone derivatives they all take a square planar structure, as seen from their electronic spectra.     

Triazamacrocyclic complexes with 8- and 9-membered chelate rings. Preparation, structures and agostic interactions in complexes of 1,5,9-triazacyclotetradecane and 1,5,9-triazacyclopentadecane

Cobalt(II), copper(II) and nickel(II) complexes of the ligands 1,5,9-triazacyclotetradecane (tatd) and 1,5,9-triazacyclopentadecane (tapd), which have 8- and 9-membered chelate rings, respectively, have been prepared and characterised. Crystal structures of [Ni(tatd)(NCS)₂]·H₂O and [Co(tatd)(NCS)₂] have been determined. The nickel(II) complex has a distorted square pyramidal geometry and the cobalt(II) complex has a distorted trigonal bipyramidal geometry. Agostic interactions between a hydrogen on the central carbon of the 8-membered chelate ring and the metal ion are observed in both complexes.     

The magnetic and electronic properties of Methanobacterium thermoautotrophicum (strain delta H) methyl coenzyme M reductase and its nickel tetrapyrrole cofactor F430. A low temperature magnetic circular dichroism study

Variable temperature magnetic circular dichroism (MCD) spectroscopy has been used to characterize the magnetic and electronic properties of the Ni(II) tetrapyrrole, F430, which is the cofactor of the S-methyl coenzyme M methylreductase enzyme from Methanobacterium thermoautotrophicum (strain delta H). 4-Coordinate forms are found to be diamagnetic (S = 0 ground state), whereas 6-coordinate forms are paramagnetic (S = 1 ground state). MCD studies, together with parallel low temperature UV-visible absorption and resonance Raman investigations, show that the equilibrium distribution of 4-coordinate square-planar and 6-coordinate bis-aquo forms of the native isomer of F430 in aqueous solution is affected by both temperature and the presence of glycerol. In the presence of 50% glycerol, the 12,13-diepimer of F430 is shown to be partially 6-coordinate in frozen solution at low temperature. Low temperature MCD magnetization data allow the determination of the axial zero-field splitting (D) of the S = 1 ground state of bis-ligand complexes of F430. The value of D is sensitive to the nature of the Ni(II) axial ligands: bis-aquo F430, D = +9 +/- 1 cm-1; bis-imidazole F430, D = -8 +/- 2 cm-1. Measurement of D = +10 +/- 1 cm-1 for F430 in the methylreductase holoenzyme argues strongly against histidine imidazole coordination to Ni(II) in the enzyme. The possible existence of alcoholic or phenolic oxygen-containing ligands (serine, threonine, tyrosine, water) to Ni(II) in the enzyme-bound cofactor is discussed.     

Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray versus molecular dynamics

The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme. Here, we analyze conformational flexibility of the side chains of the 14 conserved aromatic residues in the active-site gorge of Torpedo californica AChE based on the 47 three-dimensional crystal structures available for the native enzyme, and for its complexes and conjugates, and on a 20-ns molecular dynamics (MD) trajectory of the native enzyme. The degree of flexibility of these 14 aromatic side chains is diverse. Although the side-chain conformations of F330 and W279 are both very flexible, the side-chain conformations of F120, W233, W432, Y70, Y121, F288, F290 and F331 appear to be fixed. Residues located on, or adjacent to, the Ω-loop (C67-C94), namely W84, Y130, Y442, and Y334, display different flexibilities in the MD simulations and in the crystal structures. An important outcome of our study is that the majority of the side-chain conformations observed in the 47 Torpedo californica AChE crystal structures are faithfully reproduced by the MD simulation on the native enzyme. Thus, the protein can assume these conformations even in the absence of the ligand that permitted their experimental detection. These observations are pertinent to structure-based drug design.     

Evidence for the involvement of corrinoids and factor F430 in the reductive dechlorination of 1,2-dichloroethane by Methanosarcina barkeri.

Cobalamin and the native and diepimeric forms of factor F430 catalyzed the reductive dechlorination of 1,2-dichloroethane (1,2-DCA) to ethylene or chloroethane (CA) in a buffer with Ti(III) citrate as the electron donor. Ethylene was the major product in the cobalamin-catalyzed transformation, and the ratio of ethylene to CA formed was 25:1. Native F430 and 12,13-di-epi-F430 produced ethylene and CA in ratios of about 2:1 and 1:1, respectively. Cobalamin dechlorinated 1,2-DCA much faster than did factor F430. Dechlorination rates by all three catalysts showed a distinct pH dependence, correlated in a linear manner with the catalyst concentration and doubled with a temperature increase of 10 degrees C. Crude and boiled cell extracts of Methanosarcina barkeri also dechlorinated 1,2-DCA to ethylene and CA with Ti(III) citrate as the reductant. The catalytic components in boiled extracts were heat and oxygen stable and had low molecular masses. Fractionation of boiled extracts by a hydrophobic interaction column revealed that part of the dechlorinating components had a hydrophilic and part had a hydrophobic character. These chemical properties of the dechlorinating components and spectral analysis of boiled extracts indicated that corrinoids or factor F430 was responsible for the dechlorinations. The ratios of 3:1 to 7:1 of ethylene and CA formed by cell extracts suggested that both cofactors were concomitantly active.     

On the bioreactivity of triorganotin aminobenzoates. Investigation of trialkyl and triarylyltin(IV) esters of 3-amino and 4-aminobenzoic acids

The synthesis and study of trimethyl-, tributyl- and triphenyltin esters of the 3- and 4-aminobenzoic acids are reported. The triorganotin derivatives are characterized by elemental analyses, FT-IR and solution ¹H and ¹³C NMR spectra. The structure of the trimethyltin 4-aminobenzoate is solved by X-ray diffraction and proves to be polymeric in nature with bridging carboxylates and trigonal bipyramidal tin(IV) environment. However, all the compounds become monomeric in solution with a tetrahedral tin coordination environment in chloroform and trigonal bipyramidal in DMSO due to coordination of the solvent as the NMR spectra have revealed. The compounds exhibit variable cytotoxic activity when tested against Κ562 myelogenous leukaemia, HeLa cervical cancer and HepG2 hepatocellular carcinoma cell lines, with the butyl derivatives being the more effective and the methyl ones the less. Interestingly, their antibacterial action was significantly lower when tested against Escherichia coli, while not appreciable direct interaction with DNA has been observed. The above observations account for a mode of action that may be related to their potential interaction with cell membranes and the subsequent inhibition of various signaling processes.     

Nickel dependence of factor F430 content in Methanobacterium thermoautotrophicum

Factor F₄₃₀ is a yellow compound of unknown structure present in methanogenic bacteria. It has recently been shown to contain nickel. In this communication the influence of the nickel concentration in the growth medium on the factor F₄₃₀ content of Methanobacterium thermoautotrophicum and on the nickel content of factor F₄₃₀ was studied. It was found: (1) The content of factor F₄₃₀ in the cells was strongly dependent on the nickel concentration of the growth medium. Cells grown on media with 2.5 M NiCl₂ contained 28 times as much factor F₄₃₀ per g as those grown on media with 0.075 M NiCl₂; (2) factor F₄₃₀ was synthesized in nickel deprived cells only upon the addition of nickel Nickel uptake paralleled factor F₄₃₀ synthesis; (3) independent of the nickel concentration in the growth medium, the extinction coefficient at 430 nm of factor F₄₃₀ per mol nickel was always near 22,500 cm^-1 (mol Ni)^-1. These findings indicate that nickel is an essential component of factor F₄₃₀.Dedicated to Professor Otto Kandler on the occasion of his 60th birthday     

Biosynthesis of coenzyme F430 in methanogenic bacteria. Identification of 15,17(3)-seco-F430-17(3)-acid as an intermediate

Coenzyme F430 is a hydroporphinoid nickel complex present in all methanogenic bacteria. It is part of the enzyme system which catalyzes methane formation from methyl-coenzyme M. We describe here that under certain conditions a second nickel porphinoid accumulates in methanogenic bacteria. The compound was identified at 15,17(3)-seco-F430-17(3)-acid. The structural assignment rests on 14C-labelling experiments, fast-atom-bombardment mass spectra, 1H-NMR spectra of the corresponding hexamethyl ester, and ultraviolet/visible spectral comparison with model compounds. In cell extracts and in intact cells of methanogenic bacteria, 15,17(3)-seco-F430-17(3)-acid was converted to F430. These findings indicate that the new nickel-containing porphinoid is an intermediate in the biosynthesis of coenzyme F430.     

Structural investigations on diorganotin and triorganotin(IV) phosphomycin derivatives

Four new diorganotin(IV), (R = Me, Bu), and triorganotin(IV), (R = Me, Ph), derivatives of the phosphomycin disodium salt antibiotic[(1R,2S)-1,2-epoxypropylphosphonate]Na₂ have been synthesized and their solid state configuration studied by X-ray crystallography, FT-IR, Mössbauer, UV-Vis spectroscopies. The X-ray diffraction investigation, performed on the bis[trimethyltin(IV)]phosphomycin, showed that the coordination geometry at all the Sn atoms is trigonal bipyramidal. The structure of the complex forms an unusual polymeric zig-zag planar network. The FT-IR and the ¹¹⁹Sn Mössbauer studies supported the formation of trigonal bipyramidal (Tbp) molecular structures, both in the diorganotin(IV) and triorganotin(IV) derivatives, even if, in the case of diorganotin(IV) derivatives, the tetrahedral structure cannot be a priori excluded. The group of phosphomycin coordinates the organotin(IV) centers originating a monodimensional polymeric network, as inferred by variable temperature ¹¹⁹Sn Mössbauer spectroscopy, used to investigate lattice dynamics of the bis-[trimethyltin(IV)]phosphomycin complex.     

Nickel requirement and factor F430 content of methanogenic bacteria.

Methanobacterium thermoautotrophicum has been reported to require nickel for growth and to contain high concentrations of a nickel tetrapyrrole designated factor F430. In this communication it is shown that all methanogenic bacteria investigated incorporated nickel during growth and also synthesized factor F430. This was also true for Methanobrevibacter smithii, which is dependent on acetate as a carbon source, and for Methanosarcina barkeri growing on acetate or methanol as energy sources. Other bacteria, including Acetobacterium woodii and Clostridium thermoaceticum, contained no factor F430. It is further shown that two yellow nickel-containing degradation products were formed from factor F430 when heated at pH 7. This finding explains why several forms of factor F430 were found in methanogenic bacteria when a heat step was employed in the purification procedure.     

An extended-X-ray-absorption-fine-structure (e.x.a.f.s.) study of coenzyme F430 from Methanobacterium thermoautotrophicum.

Coenzyme F430 is a nickel porphinoid found in all methanogenic bacteria. Extended-X-ray-absorption-fine-structure (e.x.a.f.s.) spectra have been recorded above the nickel K-edge of coenzyme F430 and two model compounds, (5,10,15,20-tetramethylporphinato) nickel(II) and (5,10,15,20-tetramethylchlorinato)-nickel(II). The results show that the four nickel-nitrogen distances in F430 are split, with two nitrogen atoms at 0.192 nm and two at 0.210 nm.