Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme

The biosynthetic pathway of the clinically important antibiotic fosfomycin uses enzymes that catalyse reactions without precedent in biology. Among these is hydroxypropylphosphonic acid epoxidase, which represents a new subfamily of non-haem mononuclear iron enzymes. Here we present six X-ray structures of this enzyme: the apoenzyme at 2.0 A resolution; a native Fe(II)-bound form at 2.4 A resolution; a tris(hydroxymethyl)aminomethane-Co(II)-enzyme complex structure at 1.8 A resolution; a substrate-Co(II)-enzyme complex structure at 2.5 A resolution; and two substrate-Fe(II)-enzyme complexes at 2.1 and 2.3 A resolution. These structural data lead us to suggest how this enzyme is able to recognize and respond to its substrate with a conformational change that protects the radical-based intermediates formed during catalysis. Comparisons with other family members suggest why substrate binding is able to prime iron for dioxygen binding in the absence of alpha-ketoglutarate (a co-substrate required by many mononuclear iron enzymes), and how the unique epoxidation reaction of hydroxypropylphosphonic acid epoxidase may occur.     

A new synthetic approach to the ferritin core uncovers the soluble iron(III) oxo-hydroxo aggregate [Fe11O6(OH)6(O2CPh)15]

Hydrolytic polymerization of iron(III) occurs in many reactions in vivo, for example, the formation of bacterial magnetite in magnetotactic organisms, biomineralization of iron and the synthesis of the metallic core of the iron-storage protein ferritin. The ferritin core contains aggregates of up to 4,500 oxygen-bridged, octahedrally coordinated, high-spin iron(III) centres and is attached to the protein shell through carboxylate groups of amino-acid side chains. The X-ray and electron-diffraction patterns of this core resemble those of the mineral ferrihydrite, a hydrated iron oxide formed in nature, inter alia, by iron-dependent bacteria. The preparation and structural characterization of such large poly-iron aggregates has been a challenge to inorganic chemists. We have recently shown that tri- and tetranuclear iron(III) oxo complexes of the type thought to be important in ferritin-core formation can be prepared by reacting mononuclear [FeCl4]- and binuclear [Fe2OCl6]2- components in aprotic solvents (ref. 9 and S.M.G., W. H. Armstrong and S.J.L., in preparation). Here we report the discovery of a remarkable new molecule, [Fe11O6(OH)6(O2CPh)15], obtained by hydrolysis of the [Fe2O]4+ unit in the presence of limited amounts of water and carboxylate salts. The synthesis and properties of this soluble iron(III) oxohydroxo aggregate should help to elucidate the mechanism of formation of poly-iron centres.     

Structure and reactivity of a mononuclear non-haem iron(III)-peroxo complex

Oxygen-containing mononuclear iron species--iron(III)-peroxo, iron(III)-hydroperoxo and iron(IV)-oxo--are key intermediates in the catalytic activation of dioxygen by iron-containing metalloenzymes. It has been difficult to generate synthetic analogues of these three active iron-oxygen species in identical host complexes, which is necessary to elucidate changes to the structure of the iron centre during catalysis and the factors that control their chemical reactivities with substrates. Here we report the high-resolution crystal structure of a mononuclear non-haem side-on iron(III)-peroxo complex, [Fe(III)(TMC)(OO)](+). We also report a series of chemical reactions in which this iron(III)-peroxo complex is cleanly converted to the iron(III)-hydroperoxo complex, [Fe(III)(TMC)(OOH)](2+), via a short-lived intermediate on protonation. This iron(III)-hydroperoxo complex then cleanly converts to the ferryl complex, [Fe(IV)(TMC)(O)](2+), via homolytic O-O bond cleavage of the iron(III)-hydroperoxo species. All three of these iron species--the three most biologically relevant iron-oxygen intermediates--have been spectroscopically characterized; we note that they have been obtained using a simple macrocyclic ligand. We have performed relative reactivity studies on these three iron species which reveal that the iron(III)-hydroperoxo complex is the most reactive of the three in the deformylation of aldehydes and that it has a similar reactivity to the iron(IV)-oxo complex in C-H bond activation of alkylaromatics. These reactivity results demonstrate that iron(III)-hydroperoxo species are viable oxidants in both nucleophilic and electrophilic reactions by iron-containing enzymes.     

Infinite-layer iron oxide with a square-planar coordination

Conventional high-temperature reactions limit the control of coordination polyhedra in transition-metal oxides to those obtainable within the bounds of known coordination geometries for a given transition metal. For example, iron atoms are almost exclusively coordinated by three-dimensional polyhedra such as tetrahedra and octahedra. However, recent works have shown that binary metal hydrides act as reducing agents at low temperatures, allowing access to unprecedented structures. Here we show the reaction of a perovskite SrFeO3 with CaH2 to yield SrFeO2, a new compound bearing a square-planar oxygen coordination around Fe2+. SrFeO2 is isostructural with 'infinite layer' cupric oxides, and exhibits a magnetic order far above room temperature in spite of the two-dimensional structure, indicating strong in-layer magnetic interactions due to strong Fe d to O p hybridization. Surprisingly, SrFeO2 remains free from the structural instability that might well be expected at low temperatures owing to twofold orbital degeneracy in the Fe2+ ground state with D(4h) point symmetry. The reduction and the oxidation between SrFeO2 and SrFeO3 proceed via the brownmillerite-type intermediate SrFeO2.5, and start at the relatively low temperature of approximately 400 K, making the material appealing for a variety of applications, including oxygen ion conduction, oxygen gas absorption and catalysis.     

Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous

Mandelate racemase (MR) and muconate lactonizing enzyme (MLE) catalyse separate and mechanistically distinct reactions necessary for the catabolism of aromatic acids by Pseudomonas putida. The X-ray crystal structure of MR, solved at 2.5 A resolution, reveals that the secondary, tertiary and quaternary structures of MR and MLE are remarkably similar; also, MR and MLE are about 26% identical in primary structure. However, MR has no detectable MLE activity and vice versa. Thus, MR and MLE constitute the first example of enzymes that catalyse different reactions, as opposed to mechanistically identical reactions on different substrates, yet possess sufficient structural and sequence identity that they are likely to have evolved from a common ancestor. The discovery that MR and MLE catalyse different reactions but share a common structural framework has broad implications for the natural evolution of enzymes and metabolic pathways, as well as for the rational modification of enzyme activities.     

Ethylene polymerization by novel highly active iron/acetyl（imino）pyridyl complex

In recent years, significant developments have oc- curred in olefin polymerization with late-transition- metal catalyst systems, in particular, the discovery of exceptionally active catalysts based on penta- coordi- nate iron and cobalt bearing bis(imino)pyridyl triden- tate ligands with substituted aryl groups, reported in- dependently by the groups of Brookhart[1] and Gibson[2]. Following this discovery, a considerable amount of efforts have been dedicated to investigate the nature of the ac…     

酰胺类配体及锌配合物的合成、结构与电化学性能

以4-溴吡啶盐酸盐和对氨基苯甲酸为原料合成了4-(4-吡啶-4-基-苯甲酰氨基)-苯甲酸(HL). 通过溶剂热法合成得到配合物 [Zn2L2(CO3)(H2O)2]n (1). X-射线单晶衍射分析表明:配合物1结晶于单斜晶系P21/c空间群,结构中存在由Zn(II)离子与碳酸根氧原子形成的无机链,这些ZnO无机链进一步被配体L-中的羧基氧原子和吡啶氮原子连接,形成4-连接66拓扑的三维网络结构. 将配合物1直接作为锂离子电池负极材料,并对其电化学性能做初步研究.     

Kemp elimination catalysts by computational enzyme design

The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a >200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of >10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.     

氧桥联双核铁(Ⅲ)配合物[Fe_2(μ-O)(salphen)_2]·3H_2O的合成和晶体结构

合成了铁与配体双水杨醛缩邻苯二胺的配合物[Fe2(μ-O)(salphen)2].3H2O。该配合物晶体属三斜晶系,P1空间群,晶胞参数a=1.3257(5)nm,b=1.3311(8)nm,c=1.3921(5)nm,α=114.175(8)°,β=118.393(5)°,γ=91.537(8)°,V=1.8949(15)nm3,Dc=1.420 Mg.m-3,Z=2,F(000)=836,最终GooF=0.931,偏离因子R1=0.0967,ωR2=0.2464。分子中氧原子桥联两个铁(Ⅲ)原子,salphen上的2个氮原子和2个氧原子分别占据铁(Ⅲ)原子的其余4个配位位置,形成5配位变形四方锥结构。     

Availability and toxicity of Fe(II) and Fe(III) in Caco-2 cells

The objective of the present study was to compare the toxicity and availability of Fe(II) and Fe(III) to Caco-2 cells. Cellular damage was studied by measuring cell proliferation and lactate dehydrogenase (LDH) release. The activities of two major antioxidative enzymes [superoxide dismutase (SOD) and glutathione peroxidase (GPx)] and differentiation marker (alkaline phosphatase) were determined after the cells were exposed to different levels of iron salts. The cellular iron concentration was investigated to evaluate iron bioavailability. The results show that iron uptake of the cells treated with Fe(II) is significantly higher than that of the cells treated with Fe(III) (P<0.05). Fe(II) at a concentration >1.5 mmol/L was found to be more effective in reducing cellular viability than Fe(III). LDH release investigation suggests that Fe(II) can reduce stability of the cell membrane. The activities of SOD and GPx of the cells treated with Fe(II) were higher than those of the cells treated with Fe(III), although both of them increased with raising iron supply levels. The results indicate that both Fe(II) and Fe(III) could reduce the cellular antioxidase gene expression at high levels.     

Fe掺杂SBA-15的合成、表征及催化苯制苯酚的研究

以聚氧乙烯-聚氧丙烯-聚氧乙烯(P123)嵌段共聚物表面活性剂为模板剂,正硅酸乙酯(TEOS)为硅源,Fe( NO3)3·9H2O为铁源在酸性条件下合成Fe-SBA-15介孔分子筛.通过XRD,N2吸附-脱附,红外等分析手段对样品进行了表征.结果表明合成的样品具有有序的六方介孔结构.铁含量的不同对SBA-15的孔径及其比表面积均有影响.所合成的材料在苯羟基化反应中表现出良好的催化活性,最高转化率可达32.16％.     

Structure and assembly of protocatechuate 3,4-dioxygenase

Dioxygenases catalyse the cleavage of molecular oxygen with subsequent incorporation of both oxygen atoms into organic substrates. Some of the best-studied dioxygenases have been isolated from bacteria where they catalyse the critical ring-opening step in the biodegradation of aromatic compounds. These bacterial enzymes generally contain nonheme ferric iron as the sole cofactor. Protocatechuate 3,4-dioxygenase (3,4-PCD) was one of the first such enzymes recognized and catalyses the intradiol cleavage of protocatechuic acid by oxygen to produce beta-carboxy-cis,cis-muconic acid. Previous studies have shown that the 3,4-PCD found in Pseudomonas aeruginosa is an oligomer with a relative molecular mass (Mr) of 587,000 (587K) containing 12 copies each of alpha (22.3K) and beta (26.6K) subunits. The X-ray structure determination of 3,4-PCD reveals the catalytic iron environment required for oxygenolytic cleavage of aromatic rings and also provides a novel holoenzyme assembly with cubic 23(T) symmetry and first examples of mixed beta-barrel domains.     

Convergent evolution of similar function in two structurally divergent enzymes

An example of two related enzymes that catalyse similar reactions but possess different active sites is provided by comparing the structure of Escherichia coli thioredoxin reductase with glutathione reductase. Both are dimeric enzymes that catalyse the reduction of disulphides by pyridine nucleotides through an enzyme disulphide and a flavin. Human glutathione reductase contains four structural domains within each molecule: the flavin-adenine dinucleotide (FAD)- and nicotinamide-adenine dinucleotide phosphate (NADPH)-binding domains, the 'central' domain and the C-terminal domain that provides the dimer interface and part of the active site. Although both enzymes share the same catalytic mechanism and similar tertiary structures, their active sites do not resemble each other. We have determined the crystal structure of E. coli thioredoxin reductase at 2 A resolution, and show that thioredoxin reductase lacks the domain that provides the dimer interface in glutathione reductase, and forms a completely different dimeric structure. The catalytically active disulphides are located in different domains on opposite sides of the flavin ring system. This suggests that these enzymes diverged from an ancestral nucleotide-binding protein and acquired their disulphide reductase activities independently.     

四苯卟啉及其金属配合物对Fe~(3+)离子在水/硝基苯界面迁移的推动作用

关于四苯卟啉(H_2TPP)及其第一过渡金属配合物(MTPP,M=Mn,FeCl,Co,Ni,Cu,Zn)对H~+通过W/NB界面所产生的推动作用前文已作报道。本文研究上述两者对Fe~(3+)在W/NB界面迁移的影响,并根据实验事实提出可能的微观机理。 实验仪器、电化学测试方法及主要试剂的制备、纯化参照前文。主要结果如下。H_2TPP对Fe~(3+)在W/NB界面迁移的影响     

镍硫化物在酸性氯化物溶液中腐蚀溶出——(Ⅱ)镍锍溶出

利用玻璃隔膜电解池研究了酸性氯化物水溶液体系中镍锍与Cu~(2 )/Cu~ 偶合反应速度。在25℃至60℃的温度范围内,随着反应温度的升高,阴极极化减小,阳极极化增大,镍锍溶解速度也随之增大。阴极反应速度受铜离子液相扩散和电化学极化混合控制。该过程可用一个电化学模型描述,旋转圆盘实验数据表明,模型与实际过程相符合。     

Interactively interfacial reaction of iron-reducing bacterium and goethite for reductive dechlorination of chlorinated organic compounds

The interactively interfacial reactions between the iron-reducing bacterium （Shewanella decolorationis, S12） and iron oxide （α-FeOOH） were investigated to determine reductive dechlorination transformation of chlorinated organic compounds （chloroform and pentachlorophenol）. The results showed that the interactive system of S12＋ α-FeOOH exhibited relatively high dechlorination rate. By comparison, the S12 biotic system alone had no obvious dechlorination, and the α-FeOOH abiotic system showed low dechlorination rate. The enhanced dechlorination of chloroform and pentachlorophenol in the interactive system of S12＋α-FeOOH was derived from the promoted generation of adsorbed Fe（Ⅱ） by S12. A decrease in redox potential of the Fe （Ⅲ）/Fe （Ⅱ） couple in the interactive reaction system was determined by cyclic voltammetry. Our results will give new insight into interactively interfacial reaction between iron-reducing bacterium and iron oxides for degradation of chlorinated organic compounds under anaerobic condition.     

Photochemical cycling of iron in the surface ocean mediated by microbial iron(III)-binding ligands

Iron is a limiting nutrient for primary production in large areas of the oceans. Dissolved iron(III) in the upper oceans occurs almost entirely in the form of complexes with strong organic ligands presumed to be of biological origin. Although the importance of organic ligands to aquatic iron cycling is becoming clear, the mechanism by which they are involved in this process remains uncertain. Here we report observations of photochemical reactions involving Fe(III) bound to siderophores--high-affinity iron(III) ligands produced by bacteria to facilitate iron acquisition. We show that photolysis of Fe(III)-siderophore complexes leads to the formation of lower-affinity Fe(III) ligands and the reduction of Fe(III), increasing the availability of siderophore-bound iron for uptake by planktonic assemblages. These photochemical reactions are mediated by the alpha-hydroxy acid moiety, a group which has generally been found to be present in the marine siderophores that have been characterized. We suggest that Fe(III)-binding ligands can enhance the photolytic production of reactive iron species in the euphotic zone and so influence iron availability in aquatic systems.     

大型厌氧填埋场中铁的分布特征及迁移行为研究

以北京南郊某大型厌氧填埋场为例, 对不同填埋龄垃圾中的铁含量、价态转换及形态分布进行研究。结果表明, 该厌氧填埋场填埋龄为3~10年的垃圾中Fe含量变化范围为18532.8~26897.2 mg/kg。由于微生物的异化铁还原作用, Fe(III)不断被还原为Fe(II), Fe(II)/ Fe(III)从0.51上升到1.01。形态分析结果表明: Fe在不同填埋龄垃圾中的形态分布规律基本一致, 残渣态含量最高, 可氧化态和可还原态次之, 酸可溶解态含量最低, 可还原态受环境因素影响极大, 硫化物对Fe形态分布影响最显著。     

Reverse self-splicing of group II intron RNAs in vitro.

Group II introns, which are classed together on the basis of a conserved secondary structure, are found in organellar genes of lower eukaryotes and plants. Like introns in nuclear pre-messenger RNA, they are excised by a two-step splicing reaction to generate branched circular RNAs, the so-called lariats. A remarkable feature of group II introns is their self-splicing activity in vitro. In the absence of a nucleotide cofactor, the intron RNAs catalyse two successive transesterification reactions which lead to autocatalytic excision of the lariat IVS from pre-mRNA and concomitantly to exon ligation. By virtue of its ability to specifically bind the 5' exon, the intron can also catalyse such reactions on exogenous RNA substrates. This sequence-specific attachment could enable group II introns to integrate into unrelated RNAs by reverse splicing, in a process similar to that described for the self-splicing Tetrahymena group I intron. Here we report that group II lariat IVS can indeed reintegrate itself into an RNA composed of the ligated exons in vitro. This occurs by a process of self-splicing that completely reverses both transesterification steps of the forward reaction: it involves a transition of the 2'-5' phosphodiester bond of the lariat RNA into the 3'-5' bond of the reconstituted 5' splice junction.     

Structural insights into the stereochemistry of the cyclooxygenase reaction

Cyclooxygenases are bifunctional enzymes that catalyse the first committed step in the synthesis of prostaglandins, thromboxanes and other eicosanoids. The two known cyclooxygenases isoforms share a high degree of amino-acid sequence similarity, structural topology and an identical catalytic mechanism. Cyclooxygenase enzymes catalyse two sequential reactions in spatially distinct, but mechanistically coupled active sites. The initial cyclooxygenase reaction converts arachidonic acid (which is achiral) to prostaglandin G2 (which has five chiral centres). The subsequent peroxidase reaction reduces prostaglandin G2 to prostaglandin H2. Here we report the co-crystal structures of murine apo-cyclooxygenase-2 in complex with arachidonic acid and prostaglandin. These structures suggest the molecular basis for the stereospecificity of prostaglandin G2 synthesis.