Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation

Evolution of flavone synthase I from parsley flavanone 3beta-hydroxylase by site-directed mutagenesis

Flavanone 3beta-hydroxylase (FHT) and flavone synthase I (FNS I) are 2-oxoglutarate-dependent dioxygenases with 80% sequence identity, which catalyze distinct reactions in flavonoid biosynthesis. However, FNS I has been reported exclusively from a few Apiaceae species, whereas FHTs are more abundant. Domain-swapping experiments joining the N terminus of parsley (Petroselinum crispum) FHT with the C terminus of parsley FNS I and vice versa revealed that the C-terminal portion is not essential for FNS I activity. Sequence alignments identified 26 amino acid substitutions conserved in FHT versus FNS I genes. Homology modeling, based on the related anthocyanidin synthase structure, assigned seven of these amino acids (FHT/FNS I, M106T, I115T, V116I, I131F, D195E, V200I, L215V, and K216R) to the active site. Accordingly, FHT was modified by site-directed mutagenesis, creating mutants encoding from one to seven substitutions, which were expressed in yeast (Saccharomyces cerevisiae) for FNS I and FHT assays. The exchange I131F in combination with either M106T and D195E or L215V and K216R replacements was sufficient to confer some FNS I side activity. Introduction of all seven FNS I substitutions into the FHT sequence, however, caused a nearly complete change in enzyme activity from FHT to FNS I. Both FHT and FNS I were proposed to initially withdraw the beta-face-configured hydrogen from carbon-3 of the naringenin substrate. Our results suggest that the 7-fold substitution affects the orientation of the substrate in the active-site pocket such that this is followed by syn-elimination of hydrogen from carbon-2 (FNS I reaction) rather than the rebound hydroxylation of carbon-3 (FHT reaction).

VTVH-MCD and DFT studies of thiolate bonding to [FeNO]7/[FeO2]8 complexes of isopenicillin N synthase: substrate determination of oxidase versus oxygenase activity in nonheme Fe enzymes

Isopenicillin N synthase (IPNS) is a unique mononuclear nonheme Fe enzyme that catalyzes the four-electron oxidative double ring closure of its substrate ACV. A combination of spectroscopic techniques including EPR, absorbance, circular dichroism (CD), magnetic CD, and variable-temperature, variable-field MCD (VTVH-MCD) were used to evaluate the geometric and electronic structure of the [FeNO]7 complex of IPNS coordinated with the ACV thiolate ligand. Density Function Theory (DFT) calculations correlated to the spectroscopic data were used to generate an experimentally calibrated bonding description of the Fe-IPNS-ACV-NO complex. New spectroscopic features introduced by the binding of the ACV thiolate at 13 100 and 19 800 cm-1 are assigned as the NO pi*(ip) --> Fe dx2-y2 and S pi--> Fe dx2-y2 charge transfer (CT) transitions, respectively. Configuration interaction mixes S CT character into the NO pi*(ip) --> Fe dx2-y2 CT transition, which is observed experimentally from the VTVH-MCD data from this transition. Calculations on the hypothetical {FeO2}8 complex of Fe-IPNS-ACV reveal that the configuration interaction present in the [FeNO]7 complex results in an unoccupied frontier molecular orbital (FMO) with correct orientation and distal O character for H-atom abstraction from the ACV substrate. The energetics of NO/O2 binding to Fe-IPNS-ACV were evaluated and demonstrate that charge donation from the ACV thiolate ligand renders the formation of the FeIII-superoxide complex energetically favorable, driving the reaction at the Fe center. This single center reaction allows IPNS to avoid the O2 bridged binding generally invoked in other nonheme Fe enzymes that leads to oxygen insertion (i.e., oxygenase function) and determines the oxidase activity of IPNS.

EPR and UV-vis studies of the nitric oxide adducts of bacterial phenylalanine hydroxylase: effects of cofactor and substrate on the iron environment

Phenylalanine hydroxylase from Chromobacterium violaceum (cPAH), which catalyzes phenylalanine oxidation to tyrosine, is homologous to the catalytic domain of eukaryotic PAHs. Previous crystallographic and spectroscopic studies on mammalian PAH conflict on whether O2 binds to the open-coordination site or displaces the remaining water ligand to yield either a six- or a five-coordinate iron, respectively. The abilities of nitric oxide to behave as an oxygen mimic and a spectroscopic probe of ferrous iron are used to investigate the geometric and electronic effects of cofactor and substrate binding to cPAH by electron paramagnetic resonance (EPR) and UV-vis spectroscopies. A rhombic distortion observed for the ternary complex is due to two factors: a decrease in the Fe-NO angle and an alteration in the equatorial ligand geometry. Both factors are consistent with NO displacing the sole remaining water ligand to yield a five-coordinate iron center. Hyperfine broadening of the EPR resonances of the nitrosyl complexes by 17O-enriched water is observed in the absence of substrates or presence of cofactor only (binary complex), demonstrating that water is bound to the Fe(II). However, in the presence of substrate and cofactor (ternary complex), the EPR resonances of the nitrosyl complex are not broadened by 17O-enriched water, indicating the displacement of water by NO to afford a five-coordinate iron. Furthermore, the increased intensity in the 500-600 nm range of the UV-vis spectrum of the ternary nitrosyl complex indicates an increased overlap between the in-plane NO 2pi and d(x2-y2) and d(xz) orbitals, which corroborates a five-coordinate iron.

Enzymatic C–H activation by metal–superoxo intermediates

The mechanisms of four enzymes that initiate oxidation of their substrates by using mid-valent metal-superoxo intermediates, rather than the more frequently described high-valent iron-oxo complexes, to cleave relatively strong C-H bonds have come into focus in the past several years. In two of these reactions, the alternative manifold for O2 and C-H activation enables unique four-electron oxidation reactions, thus significantly augmenting Nature's arsenal for transformation of aliphatic carbon compounds. General principles of this alternative manifold, including common kinetic characteristics and thermodynamic limitations, are emerging. Recent, combined experimental and computational studies on other systems have shown how a more thorough understanding of the structures of the metal-superoxo intermediates and the mechanisms by which they cleave C-H bonds might be achieved.

Hypoxia inducible factor prolyl 4-hydroxylase enzymes: center stage in the battle against hypoxia, metabolic compromise and oxidative stress

Studies of adaptive mechanisms to hypoxia led to the discovery of the transcription factor called hypoxia inducible factor (HIF). HIF is a ubiquitously expressed, heterodimeric transcription factor that regulates a cassette of genes that can provide compensation for hypoxia, metabolic compromise, and oxidative stress including erythropoietin, vascular endothelial growth factor, or glycolytic enzymes. Diseases associated with oxygen deprivation and consequent metabolic compromise such as stroke or Alzheimer's disease may result from inadequate engagement of adaptive signaling pathways that culminate in HIF activation. The discovery that HIF stability and activation are governed by a family of dioxygenases called HIF prolyl 4 hydroxylases (PHDs) identified a new target to augment the transcriptional activity of HIF and thus the adaptive machinery that governs neuroprotection. PHDs lose activity when cells are deprived of oxygen, iron or 2-oxoglutarate. Inhibition of PHD activity triggers the cellular homeostatic response to oxygen and glucose deprivation by stabilizing HIF and other proteins. Herein, we discuss the possible role of PHDs in regulation of both HIF-dependent and -independent cell survival pathways in the nervous system with particular attention to the co-substrate requirements for these enzymes. The emergence of neuroprotective therapies that modulate genes capable of combating metabolic compromise is an affirmation of elegant studies done by John Blass and colleagues over the past five decades implicating altered metabolism in neurodegeneration.

Modeling the 2-His-1-Carboxylate Facial Triad: Iron−Catecholato Complexes as Structural and Functional Models of the Extradiol Cleaving Dioxygenases

Mononuclear iron(II)- and iron(III)-catecholato complexes with three members of a new 3,3-bis(1-alkylimidazol-2-yl)propionate ligand family have been synthesized as models of the active sites of the extradiol cleaving catechol dioxygenases. These enzymes are part of the superfamily of dioxygen-activating mononuclear non-heme iron enzymes that feature the so-called 2-His-1-carboxylate facial triad. The tridentate, tripodal, and monoanionic ligands used in this study include the biologically relevant carboxylate and imidazole donor groups. The structure of the mononuclear iron(III)-tetrachlorocatecholato complex [Fe(L3)(tcc)(H2O)] was determined by single-crystal X-ray diffraction, which shows a facial N,N,O capping mode of the ligand. For the first time, a mononuclear iron complex has been synthesized, which is facially capped by a ligand offering a tridentate Nim,Nim,Ocarb donor set, identical to the endogenous ligands of the 2-His-1-carboxylate facial triad. The iron complexes are five-coordinate in noncoordinating media, and the vacant coordination site is accessible for Lewis bases, e.g., pyridine, or small molecules such as dioxygen. The iron(II)-catecholato complexes react with dioxygen in two steps. In the first reaction the iron(II)-catecholato complexes rapidly convert to the corresponding iron(III) complexes, which then, in a second slow reaction, exhibit both oxidative cleavage and auto-oxidation of the substrate. Extradiol and intradiol cleavage are observed in noncoordinating solvents. The addition of a proton donor results in an increase in extradiol cleavage. The complexes add a new example to the small group of synthetic iron complexes capable of eliciting extradiol-type cleavage and provide more insight into the factors determining the regioselectivity of the enzymes.

Lys296 and Arg299 residues in the C-terminus of MD-ACO1 are essential for a 1-aminocyclopropane-1-carboxylate oxidase enzyme activity

The 1-aminocyclopropane-1-carboxylate (ACC) oxidase catalyzes the last step in the biosynthesis of ethylene from ACC in higher plants. The complex structure of ACC oxidase/Fe(2+)/H(2)O derived from Petunia hybrida has recently been established by X-ray crystallography and it provides a vast structural information for ACC oxidase. Our mutagenesis study shows that both Lys296 and Arg299 residues in the C-terminal helix play important roles in enzyme activity. Both K296R and R299K mutant proteins retain only 30-15% of their enzyme activities with respect to that of the wild-type, implying that the positive charges of C-terminal residues are involved in enzymatic reaction. Furthermore, the sequence alignment of ACC oxidases from 24 different species indicates an existence of the exclusively conserved motif (Lys296-Glu301) especially in the C-terminus. The structure model based on our findings suggests that the positive-charged surface in the C-terminal helix of the ACC oxidase could be a major stabilizer in the spatial arrangement of reactants and that the positive-charge network between the active site and C-terminus is critical for ACC oxidase activity.

Mass spectrometry of protein modifications by reactive oxygen and nitrogen species

The modification of proteins by reactive oxygen and nitrogen species plays an important role in various biologic processes involving protein activation and inactivation, protein translocation and turnover during signal transduction, stress response, proliferation, and apoptosis. Recent advances in protein and peptide separation and mass spectrometry provide increasingly sophisticated tools for the quantitative analysis of such protein modifications, which are absolutely necessary for their correlation with biologic phenomena. The present review focuses specifically on the qualitative and quantitative mass spectrometric analysis of the most common protein modifications caused by reactive oxygen and nitrogen species in vivo and in vitro and details a case study on a membrane protein the sarco/endoplasmic reticulum Ca-ATPase (SERCA).

Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase

The Fe(II)- and alpha-ketoglutarate (alphaKG)-dependent dioxygenases use mononuclear nonheme iron centers to effect hydroxylation of their substrates and decarboxylation of their cosubstrate, alphaKG, to CO(2) and succinate. Our recent dissection of the mechanism of taurine:alphaKG dioxygenase (TauD), a member of this enzyme family, revealed that two transient complexes accumulate during catalysis in the presence of saturating substrates. The first complex contains the long-postulated C-H-cleaving Fe(IV)-oxo intermediate, J, and the second is an enzyme.product(s) complex. Here, we demonstrate the accumulation of two transient complexes in the reaction of a prolyl-4-hydroxylase (P4H), a functional homologue of human alphaKG-dependent dioxygenases with essential roles in collagen biosynthesis and oxygen sensing. The kinetic and spectroscopic properties of these two P4H complexes suggest that they are homologues of the TauD intermediates. Most notably, the first exhibits optical absorption and Mössbauer spectra similar to those of J and, like J, a large substrate deuterium kinetic isotope on its decay. The close correspondence of the accumulating states in the P4H and TauD reactions supports the hypothesis of a conserved mechanism for substrate hydroxylation by enzymes in this family.

Structural studies on 2-oxoglutarate oxygenases and related double-stranded β-helix fold proteins

Mononuclear non-heme ferrous iron dependent oxygenases and oxidases constitute an extended enzyme family that catalyze a wide range of oxidation reactions. The largest known sub-group employs 2-oxoglutarate as a cosubstrate and catalysis by these and closely related enzymes is proposed to proceed via a ferryl intermediate coordinated to the active site via a conserved HXD/E...H motif. Crystallographic studies on the 2-oxoglutarate oxygenases and related enzymes have revealed a common double-stranded beta-helix core fold that supports the residues coordinating the iron. This fold is common to proteins of the cupin and the JmjC transcription factor families. The crystallographic studies on 2-oxoglutarate oxygenases and closely related enzymes are reviewed and compared with other metallo-enzymes/related proteins containing a double-stranded beta-helix fold. Proposals regarding the suitability of the active sites and folds of the 2-oxoglutarate oxygenases to catalyze reactions involving reactive oxidizing species are described.

Unexpected Oxidation of a Depsipeptide Substrate Analogue in Crystalline Isopenicillin N Synthase

Isopenicillin N synthase (IPNS) is a non-heme iron(ii)-dependent oxidase that is central to penicillin biosynthesis. Herein, we report mechanistic studies of the IPNS reaction in the crystalline state, using the substrate analogue delta-(L-alpha-aminoadipoyl)-(3R)-methyl-L-cysteine D-alpha-hydroxyisovaleryl ester (AmCOV) to probe the early stages of the catalytic cycle. The X-ray crystal structure of the anaerobic IPNS:Fe(II):AmCOV complex was solved to 1.40 A resolution, and it reveals several subtle differences in the active site relative to the complex of the enzyme with its natural substrate. The crystalline IPNS:Fe(II):AmCOV complex was then exposed to oxygen gas at high pressure; this brought about reaction to give what appears to be a hydroxymethyl/ene-thiol product. A mechanism for this reaction is proposed. These results offer further insight into the delicate interplay of steric and electronic effects in the IPNS active site and the mechanistic intricacies of this remarkable enzyme.

Anthocyanidin synthase in non-anthocyanin-producing Caryophyllales species

Red colors in flowers are mainly produced by two types of pigments: anthocyanins and betacyanins. Although anthocyanins are widely distributed in higher plants, betacyanins have replaced anthocyanins in the Caryophyllales. There has been no report so far to find anthocyanins and betacyanins existing together within the same plant. This curious phenomenon has been examined from genetic and evolutionary perspectives, however nothing is known at the molecular level about the mutual exclusion of anthocyanins and betacyanins in higher plants. Here, we show that spinach (Spinacia oleracea) and pokeweed (Phytolacca americana), which are both members of the Caryophyllales, have functional anthocyanidin synthases (ANSs). The ability of ANSs of the Caryophyllales to oxidize trans-leucocyanidin to cyanidin is comparable to that of ANSs in anthocyanin-producing plants. Expression profiles reveal that, in spinach, dihydroflavonol 4-reductase (DFR) and ANS are not expressed in most tissues and organs, except seeds, in which ANS may contribute to proanthocyanidin synthesis. One possible explanation for the lack of anthocyanins in the Caryophyllales is the suppression or limited expression of the DFR and ANS.

Site-directed mutagenesis and spectroscopic studies of the iron-binding site of (S)-2-hydroxypropylphosphonic acid epoxidase

(S)-2-Hydroxylpropanylphosphonic acid epoxidase (HppE) is a novel type of mononuclear non-heme iron-dependent enzyme that catalyzes the O2 coupled, oxidative epoxide ring closure of HPP to form fosfomycin, which is a clinically useful antibiotic. Sequence alignment of the only two known HppE sequences led to the speculation that the conserved residues His138, Glu142, and His180 are the metal binding ligands of the Streptomyces wedmorensis enzyme. Substitution of these residues with alanine resulted in significant reduction of metal binding affinity, as indicated by EPR analysis of the enzyme-Fe(II)-substrate-nitrosyl complex and the spectral properties of the Cu(II)-reconstituted mutant proteins. The catalytic activities for both epoxidation and self-hydroxylation were also either eliminated or diminished in proportion to the iron content in these mutants. The complete loss of enzymatic activity for the E142A and H180A mutants in vivo and in vitro is consistent with the postulated roles of the altered residues in metal binding. The H138A mutant is also inactive in vivo, but in vitro it retains 27% of the active site iron and nearly 20% of the wild-type activity. Thus, it cannot be unequivocally stated whether H138 is an iron ligand or simply facilitates iron binding due to proximity. The results reported herein provide initial evidence implicating an unusual histidine/carboxylate iron ligation in HppE. By analogy with other well-characterized enzymes from the 2-His-1-carboxylate family, this type of iron core is consistent with a mechanism in which both oxygen and HPP bind to the iron as a first step in the in the conversion of HPP to fosfomycin.

Unique binding of a non-natural l,l,l-substrate by isopenicillin N synthase

Isopenicillin N synthase (IPNS) is a non-haem iron oxidase that catalyses the formation of isopenicillin N from the tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. In this report, we describe the crystal structure of the enzyme with a non-natural L,L,L-tripeptide substrate, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-L-3,3,3,3',3',3'-hexafluorovaline. This structure reveals a strong binding interaction of the tripeptide within the active site and a unique conformation for the non-natural L,L,L-diastereomer. Taken together, these findings provide a possible rationale for the previously observed inhibitory effects of L,L,L-tripeptide substrates on IPNS activity.

C-terminus mutations of Acremonium chrysogenum deacetoxy/deacetylcephalosporin C synthase with improved activity toward penicillin analogs

Deacetoxy/deacetylcephalosporin C synthase (acDAOC/DACS) from Acremonium chrysogenum is a bifunctional enzyme that catalyzes both the ring-expansion of penicillin N to deacetoxycephalosporin C (DAOC) and the hydroxylation of the latter to deacetylcephalosporin C (DAC). Three residues N305, R307 and R308 located in close proximity to the C-terminus of acDAOC/DACS were each mutated to leucine. The N305L and R308L mutant acDAOC/DACSs showed significant improvement in their ability to convert penicillin analogs. R308 was identified for the first time as a critical residue for DAOC/DACS activity. Kinetic analyses of purified R308L enzyme indicated its improved catalytic efficiency is due to combined improvements of K(m) and k(cat). Comparative modeling of acDAOC/DACS supports the involvement of R308 in the formation of substrate-binding pocket.

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.

NO binding to naphthalene dioxygenase

Nitric oxide (NO) is commonly used as an analogue for dioxygen in structural and spectroscopic studies of oxygen binding and oxygen activation. In this study, crystallographic structures of naphthalene dioxygenase (NDO) in complex with nitric oxide are reported. In the presence of the aromatic substrate indole, NO is bound end-on to the active-site mononuclear iron of NDO. The structural observations correlate well with spectroscopic measurements of NO binding to NDO in solution. However, the end-on binding of NO is in contrast to the recently reported structure of oxygen to the active-site iron of NDO that binds side-on. While NO is a good oxygen analogue with many similarities to O(2), the different binding mode of NO to the active-site iron atom leads to different mechanistic implications. Hence, caution needs to be used in extrapolating NO as an analogue to O(2) binding.

The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana

The crystal structure of the gene product of At3g21360 from Arabidopsis thaliana was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 19.3% (Rfree = 24.1%) at 2.4 A resolution. The crystal structure includes two monomers in the asymmetric unit that differ in the conformation of a flexible domain that spans residues 178-230. The crystal structure confirmed that At3g21360 encodes a protein belonging to the clavaminate synthase-like superfamily of iron(II) and 2-oxoglutarate-dependent enzymes. The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily.

ENDOR Studies of the Ligation and Structure of the Non-Heme Iron Site in ACC Oxidase

Ethylene is a plant hormone involved in all stages of growth and development, including regulation of germination, responses to environmental stress, and fruit ripening. The final step in ethylene biosynthesis, oxidation of 1-aminocyclopropane-1-carboxylic acid (ACC) to yield ethylene, is catalyzed by ACC oxidase (ACCO). In a previous EPR and ENDOR study of the EPR-active Fe(II)-nitrosyl, [FeNO],(7) complex of ACCO, we demonstrated that both the amino and the carboxyl moieties of the inhibitor d,l-alanine, and the substrate ACC by analogy, coordinate to the Fe(II) ion in the Fe(II)-NO-ACC ternary complex. In this report, we use 35 GHz pulsed and CW ENDOR spectroscopy to examine the coordination of Fe by ACCO in more detail. ENDOR data for selectively (15)N-labeled derivatives of substrate-free ACCO-NO (E-NO) and substrate/inhibitor-bound ACCO-NO (E-NO-S) have identified two histidines as protein-derived ligands to Fe; (1,2)H and (17)O ENDOR of samples in D(2)O and H(2)(17)O solvent have confirmed the presence of water in the substrate-free Fe(II) coordination sphere (E-NO). Analysis of orientation-selective (14,15)N and (17)O ENDOR data is interpreted in terms of a structural model of the ACCO active site, both in the presence (E-NO-S) and in the absence (E-NO) of substrate. Evidence is also given that substrate binding dictates the orientation of bound O(2).

Oxidation by 2-oxoglutarate oxygenases: non-haem iron systems in catalysis and signalling

The 2-oxoglutarate (2OG) and ferrous iron dependent oxygenases are a superfamily of enzymes that catalyse a wide range of reactions including hydroxylations, desaturations and oxidative ring closures. Recently, it has been discovered that they act as sensors in the hypoxic response in humans and other animals. Substrate oxidation is coupled to conversion of 2OG to succinate and carbon dioxide. Kinetic, spectroscopic and structural studies are consistent with a consensus mechanism in which ordered binding of (co)substrates enables control of reactive intermediates. Binding of the substrate to the active site triggers the enzyme for ligation of dioxygen to the metal. Oxidative decarboxylation of 2OG then generates the ferryl species thought to mediate substrate oxidation. Structural studies reveal a conserved double-stranded beta-helix core responsible for binding the iron, via a 2His-1carboxylate motif and the 2OG side chain. The rigidity of this core contrasts with the conformational flexibility of surrounding regions that are involved in binding the substrate. Here we discuss the roles of 2OG oxygenases in terms of the generic structural and mechanistic features that render the 2OG oxygenases suited for their functions.

Cupin-type phosphoglucose isomerases (Cupin-PGIs) constitute a novel metal-dependent PGI family representing a convergent line of PGI evolution

Cupin-type phosphoglucose isomerases (cPGIs) were identified in some archaeal and bacterial genomes and the respective coding function of cpgi's from the euryarchaeota Archaeoglobus fulgidus and Methanosarcina mazei, as well as the bacteria Salmonella enterica serovar Typhimurium and Ensifer meliloti, was proven by functional overexpression. These cPGIs and the cPGIs from Pyrococcus and Thermococcus spp. represent the cPGI family and were compared with respect to kinetic, inhibitory, thermophilic, and metal-binding properties. cPGIs showed a high specificity for the substrates fructose-6-phosphate and glucose-6-phosphate and were inhibited by millimolar concentrations of sorbitol-6-phosphate, erythrose-4-phosphate, and 6-phosphogluconate. Treatment of cPGIs with EDTA resulted in a complete loss of catalytic activity, which could be regained by the addition of some divalent cations, most effectively by Fe2+ and Ni2+, indicating a metal dependence of cPGI activity. The motifs TX3PX3GXEX3TXGHXHX6-11EXY and PPX3HX3N were deduced as the two signature patterns of the novel cPGI family. Phylogenetic analysis suggests lateral gene transfer for the bacterial cPGIs from euryarchaeota.

Alkylation damage in DNA and RNA--repair mechanisms and medical significance

Alkylation lesions in DNA and RNA result from endogenous compounds, environmental agents and alkylating drugs. Simple methylating agents, e.g. methylnitrosourea, tobacco-specific nitrosamines and drugs like temozolomide or streptozotocin, form adducts at N- and O-atoms in DNA bases. These lesions are mainly repaired by direct base repair, base excision repair, and to some extent by nucleotide excision repair (NER). The identified carcinogenicity of O(6)-methylguanine (O(6)-meG) is largely caused by its miscoding properties. Mutations from this lesion are prevented by O(6)-alkylG-DNA alkyltransferase (MGMT or AGT) that repairs the base in one step. However, the genotoxicity and cytotoxicity of O(6)-meG is mainly due to recognition of O(6)-meG/T (or C) mispairs by the mismatch repair system (MMR) and induction of futile repair cycles, eventually resulting in cytotoxic double-strand breaks. Therefore, inactivation of the MMR system in an AGT-defective background causes resistance to the killing effects of O(6)-alkylating agents, but not to the mutagenic effect. Bifunctional alkylating agents, such as chlorambucil or carmustine (BCNU), are commonly used anti-cancer drugs. DNA lesions caused by these agents are complex and require complex repair mechanisms. Thus, primary chloroethyl adducts at O(6)-G are repaired by AGT, while the secondary highly cytotoxic interstrand cross-links (ICLs) require nucleotide excision repair factors (e.g. XPF-ERCC1) for incision and homologous recombination to complete repair. Recently, Escherichia coli protein AlkB and human homologues were shown to be oxidative demethylases that repair cytotoxic 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) residues. Numerous AlkB homologues are found in viruses, bacteria and eukaryotes, including eight human homologues (hABH1-8). These have distinct locations in subcellular compartments and their functions are only starting to become understood. Surprisingly, AlkB and hABH3 also repair RNA. An evaluation of the biological effects of environmental mutagens, as well as understanding the mechanism of action and resistance to alkylating drugs require a detailed understanding of DNA repair processes.

The biosynthetic gene cluster for a monocyclic beta-lactam antibiotic, nocardicin A

The monocyclic beta-lactam antibiotic nocardicin A is related structurally and biologically to the bicyclic beta-lactams comprised of penicillins/cephalosporins, clavams, and carbapenems. Biosynthetic gene clusters are known for each of the latter, but not for monocyclic beta-lactams. A previously cloned gene encoding an enzyme specific to the biosynthetic pathway was used to isolate the nocardicin A cluster from Nocardia uniformis. Sequence analysis revealed the presence of 14 open reading frames involved in antibiotic production, resistance, and export. Among these are a two-protein nonribosomal peptide synthetase system, p-hydroxyphenylglycine biosynthetic genes, an S-adenosylmethionine-dependent 3-amino-3-carboxypropyl transferase (Nat), and a cytochrome P450. Gene disruption mutants of Nat, as well as an activation domain of the NRPS system, led to loss of nocardicin A formation. Several enzymes involved in antibiotic biosynthesis were heterologously overproduced, and biochemical characterization confirmed their proposed activities.

The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes

General knowledge of dioxygen-activating mononuclear non-heme iron(II) enzymes containing a 2-His-1-carboxylate facial triad has significantly expanded in the last few years, due in large part to the extensive library of crystal structures that is now available. The common structural motif utilized by this enzyme superfamily acts as a platform upon which a wide assortment of substrate transformations are catalyzed. The facial triad binds a divalent metal ion at the active site, which leaves the opposite face of the octahedron available to coordinate a variety of exogenous ligands. The binding of substrate activates the metal center for attack by dioxygen, which is subsequently converted to a high-valent iron intermediate, a formidable oxidizing species. Herein, we summarize crystallographic and mechanistic features of this metalloenzyme superfamily, which has enabled the proposal of a common but flexible pathway for dioxygen activation.

Preparation and characterization of the native iron(II)-containing DNA repair AlkB protein directly from Escherichia coli

The Escherichia coli AlkB protein was recently found to repair cytotoxic DNA lesions 1-methyladenine and 3-methylcytosine by using a novel iron-catalyzed oxidative demethylation mechanism. This protein belongs to a family of 2-ketoglutarate-Fe(II)-dependent dioxygenase proteins that utilize iron and 2-ketoglutarate to activate dioxygen for oxidation reactions. We report here the overexpression and isolation of the native Fe(II)-AlkB with a bound cofactor, 2-ketoglutarate, directly from E. coli. UV-vis measurements showed an absorption peak at 560 nm, which is characteristic of a bidentate 2-ketoglutarate bound to an iron(II) ion. Addition of excess amounts of single-stranded DNA to this isolated Fe(II)-AlkB protein caused a 9 nm shift of the 560 nm band to a higher energy, indicating a DNA-binding-induced geometry change of the active site. X-ray absorption spectra of the active site iron(II) in AlkB suggest a five-coordinate iron(II) center in the protein itself and a centrosymmetric six-coordinate iron(II) site upon addition of single-stranded DNA. This geometry change may play important roles in the DNA damage-searching and damage-repair functions of AlkB. These results provide direct evidence for DNA binding to AlkB which modulates the active site iron(II) geometry. The isolation of the native Fe(II)-AlkB also allows for further investigation of the iron(II) center and detailed mechanistic studies of the dioxygen-activation and damage-repair reactions performed by AlkB.

Active-site-mediated elimination of hydrogen fluoride from a fluorinated substrate analogue by isopenicillin N synthase

Isopenicillin N synthase (IPNS) is a non-haem iron oxidase that catalyses the formation of bicyclic isopenicillin N from delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV). In this study we report a novel activity for the iron of the IPNS active site, which behaves as a Lewis acid to catalyse the elimination of HF from the fluorinated substrate analogue, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-beta-fluorovaline (ACbetaFV). X-Ray crystallographic studies of IPNS crystals grown anaerobically with ACbetaFV reveal that the valinyl beta-fluorine is missing from the active site region, and suggest the presence of the unsaturated tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-isodehydrovaline in place of substrate ACbetaFV. (19)F NMR studies confirm the release of fluoride from ACbetaFV in the presence of the active IPNS enzyme. These results suggest a new mode of reactivity for the IPNS iron centre, a mechanism of action that has not previously been reported for any of the iron oxidase enzymes.

Gene clusters for insecticidal loline alkaloids in the grass-endophytic fungus Neotyphodium uncinatum

Loline alkaloids are produced by mutualistic fungi symbiotic with grasses, and they protect the host plants from insects. Here we identify in the fungal symbiont, Neotyphodium uncinatum, two homologous gene clusters (LOL-1 and LOL-2) associated with loline-alkaloid production. Nine genes were identified in a 25-kb region of LOL-1 and designated (in order) lolF-1, lolC-1, lolD-1, lolO-1, lolA-1, lolU-1, lolP-1, lolT-1, and lolE-1. LOL-2 contained the homologs lolC-2 through lolE-2 in the same order and orientation. Also identified was lolF-2, but its possible linkage with either cluster was undetermined. Most lol genes were regulated in N. uncinatum and N. coenophialum, and all were expressed concomitantly with loline-alkaloid biosynthesis. A lolC-2 RNA-interference (RNAi) construct was introduced into N. uncinatum, and in two independent transformants, RNAi significantly decreased lolC expression (P < 0.01) and loline-alkaloid accumulation in culture (P < 0.001) compared to vector-only controls, indicating involvement of lolC in biosynthesis of lolines. The predicted LolU protein has a DNA-binding site signature, and the relationships of other lol-gene products indicate that the pathway has evolved from various different primary and secondary biosynthesis pathways.

The enzymology of clavam and carbapenem biosynthesis

The enzyme-catalysed reactions involved in formation of the bicyclic clavam and carbapenem nuclei, including beta-amino acid and beta-lactam formation, are discussed and compared with those involved in penicillin and cephalosporin biosynthesis. The common role of unusual oxidation reactions in the biosynthetic pathways and the lack of synthetic reagents available to effect them are highlighted.

Structure–function correlations in oxygen activating non-heme iron enzymes

A large group of mononuclear non-heme iron enzymes exist which activate dioxygen to catalyze key biochemical transformations, including many of medical, pharmaceutical and environmental significance. These enzymes utilize high-spin Fe(II) active sites and additional reducing equivalents from cofactors or substrates to react with O2 to yield iron-oxygen intermediates competent to transform substrate to product. While Fe(II) sites have been difficult to study due to the lack of dominant spectroscopic features, a spectroscopic methodology has been developed which allows the elucidation of the geometric and electronic structures of these active sites and provides molecular level insight into the mechanisms of catalysis. This review provides a summary of this methodology with emphasis on its application to the determination of important active site structure-function correlations in mononuclear non-heme iron enzymes. These studies provide key insight into the mechanisms of oxygen activation, active site features that contribute to differences in reactivity and, combined with theoretical calculations and model studies, the nature of oxygen intermediates active in catalysis.

4-Hydroxyphenylpyruvate dioxygenase

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an Fe(II)-dependent, non-heme oxygenase that catalyzes the conversion of 4-hydroxyphenylpyruvate to homogentisate. This reaction involves decarboxylation, substituent migration and aromatic oxygenation in a single catalytic cycle. HPPD is a member of the alpha-keto acid dependent oxygenases that typically require an alpha-keto acid (almost exclusively alpha-ketoglutarate) and molecular oxygen to either oxygenate or oxidize a third molecule. As an exception in this class of enzymes HPPD has only two substrates, does not use alpha-ketoglutarate, and incorporates both atoms of dioxygen into the aromatic product, homogentisate. The tertiary structure of the enzyme would suggest that its mechanism converged with that of other alpha-keto acid enzymes from an extradiol dioxygenase progenitor. The transformation catalyzed by HPPD has both agricultural and therapeutic significance. HPPD catalyzes the second step in the pathway for the catabolism of tyrosine, that is common to essentially all aerobic forms of life. In plants this pathway has an anabolic branch from homogentisate that forms essential isoprenoid redox cofactors such as plastoquinone and tocopherol. Naturally occurring multi-ketone molecules act as allelopathic agents by inhibiting HPPD and preventing the production of homogentisate and hence required redox cofactors. This has been the basis for the development of a range of very effective herbicides that are currently used commercially. In humans, deficiencies of specific enzymes of the tyrosine catabolism pathway give rise to a number of severe metabolic disorders. Interestingly, HPPD inhibitor/herbicide molecules act also as therapeutic agents for a number of debilitating and lethal inborn defects in tyrosine catabolism by preventing the accumulation of toxic metabolites.

The cis-Pro touch-turn: a rare motif preferred at functional sites

A new motif of three-dimensional (3D) protein structure is described, called the cis-Pro touch-turn. In this four-residue, three-peptide motif, the central peptide is cis. Residue 2, which precedes the proline, has phi, psi values either in the "prePro region" of the Ramachandran plot near -130 degrees, 75 degrees or in the Lalpha region near +60 degrees, +60 degrees. The Calpha(1)-Calpha(4) distance is 4-5 A and the two flanking peptides lie parallel to one another, making van der Waals contact rather than a hydrogen bond. Apparently, this arrangement is locally unfavorable and therefore rare, usually occurring only if needed for biological function. Of the 12 examples in a 500-protein database, cis-Pro touch-turns are found at the catalytic sites of pectate lyase, Ni-Fe hydrogenase, glucoamylase, xylanase, and opine dehydrogenase and at the primary binding sites of ribonuclease H, type I DNA polymerase, ribotoxin, and phage gene 3 protein. In each of these protein families, the touch-turns serve different roles; their functional importance is supported by conservation and mutagenesis data. In analyzing the conservation patterns of these 3D motifs, new methods for in-depth quality evaluation of the structural bioinformatic data are employed to distinguish between significant exceptions and errors

The active site and substrate-binding mode of 1-aminocyclopropane-1-carboxylate oxidase determined by site-directed mutagenesis and comparative modelling studies

The active site and substrate-binding mode of MD-ACO1 (Malus domestica Borkh. 1-aminocyclopropane-1-carboxylate oxidase) have been determined using site-directed mutagenesis and comparative modelling methods. The MD-ACO1 protein folds into a compact jelly-roll motif comprised of eight a-helices, 12 b-strands and several long loops. The active site is well defined as a wide cleft near the C-terminus. The co-substrate ascorbate is located in cofactor Fe2+-binding pocket, the so-called '2-His-1-carboxylate facial triad'. In addition, our results reveal that Arg244 and Ser246 are involved in generating the reaction product during enzyme catalysis. The structure agrees well with the biochemical and site-directed mutagenesis results. The three-dimensional structure together with the steady-state kinetics of both the wild-type and mutant MD-ACO1 proteins reveal how the substrate specificity of MD-ACO1 is involved in the catalytic mechanism, providing insights into understanding the fruit ripening process at atomic resolution.

Conformational Flexibility of the C Terminus with Implications for Substrate Binding and Catalysis Revealed in a New Crystal Form of Deacetoxycephalosporin C Synthase

Deacetoxycephalosporin C synthase (DAOCS) from Streptomyces clavuligerus catalyses the oxidative ring expansion of the penicillin nucleus into the nucleus of cephalosporins. The reaction requires dioxygen and 2-oxoglutarate as co-substrates to create a reactive iron-oxygen intermediate from a ferrous iron in the active site. The active enzyme is monomeric in solution. The structure of DAOCS was determined earlier from merohedrally twinned crystals where the last four C-terminal residues (308-311) of one molecule penetrate the active site of a neighbouring molecule, creating a cyclic trimeric structure in the crystal. Shortening the polypeptide chain from the C terminus by more than four residues diminishes activity. Here, we describe a new crystal form of DAOCS in which trimer formation is broken and the C-terminal arm is free. These crystals show no signs of twinning, and were obtained from DAOCS labelled with an N-terminal His-tag. The modified DAOCS is catalytically active. The free C-terminal arm protrudes into the solvent, and the C-terminal domain (residues 268-299) is rotated by about 16 degrees towards the active site. The last 12 residues (300-311) are disordered. Structures for various enzyme-substrate and enzyme-product complexes in the new crystal form confirm overlapping binding sites for penicillin and 2-oxoglutarate. The results support the notion that 2-oxoglutarate and dioxygen need to react first to produce an oxidizing iron species, followed by reaction with the penicillin substrate. The position of the penicillin nucleus is topologically similar in the two crystal forms, but the penicillin side-chain in the new non-twinned crystals overlaps with the position of residues 304-306 of the C-terminal arm in the twinned crystals. An analysis of the interactions between the C-terminal region and residues in the active site indicates that DAOCS could also accept polypeptide chains as ligands, and these could bind near the iron.

Crystal Structure and Mechanistic Implications of 1-Aminocyclopropane-1-Carboxylic Acid Oxidase—The Ethylene-Forming Enzyme

The final step in the biosynthesis of the plant signaling molecule ethylene is catalyzed by 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO). ACCO requires bicarbonate as an activator and catalyzes the oxidation of ACC to give ethylene, CO2, and HCN. We report crystal structures of ACCO in apo-form (2.1 A resolution) and complexed with Fe(II) (2.55 A) or Co(II) (2.4 A). The active site contains a single Fe(II) ligated by three residues (His177, Asp179, and His234), and it is relatively open compared to those of the 2-oxoglutarate oxygenases. The side chains of Arg175 and Arg244, proposed to be involved in binding bicarbonate, project away from the active site, but conformational changes may allow either or both to enter the active site. The structures will form a basis for future mechanistic and inhibition studies.

Structures and Properties of Ruthenium(II) Complexes of Pyridylamine Ligands with Oxygen-Bound Amide Moieties: Regulation of Structures and Proton-Coupled Electron Transfer

Tris(2-pyridylemthyl)amine (TPA) derivatives having two amide moieties at the 6-positions of the two pyridine rings of TPA and their Ru(II) complexes were synthesized and characterized by spectroscopic methods, X-ray crystallography, and electrochemical measurements. The complexes prepared were [RuCl(L)]PF(6) (L = N,N-bis(6-(1-naphthoylamide)-2-pyridylmethyl)-N-(2-pyridylmethyl)amine (1), N,N-bis(6-(2-naphthoylamide)-2-pyridylmethyl)-N-(2-pyridylmethyl)amine (2), N,N-bis(6-(isobutyrylamide)-2-pyridylmethyl)-N-(2-pyridylmethyl)amine (3)); the crystal structures of the three compounds were established by X-ray crystallography. In variable-temperature (1)H NMR spectra of 1 and 2 in CD(3)CN solutions, the pi-pi stacking in 1 was too rigid to exhibit any fluxional motions in NMR measurements; however, the pi-pi stacking of 2 was weaker and showed fluxional behavior in nearly T-shaped pi-pi interaction for the 2-naphthly groups (DeltaH degrees = -2.3 kJ mol(-1); DeltaG degrees = -0.9 kJ mol(-1) and DeltaS degrees = -7.7 J mol(-1) K(-1) at 233 K in CD(3)CN). For each of these three complexes, one of the amide moieties coordinated to the Ru(II) center through an amide oxygen. The other uncoordinated amide N-H formed intramolecular hydrogen bonding which remained intact even in aqueous media, indicating the intramolecular hydrogen bonding was geometrically compelled to form. The amide coordination is also stabilized and strengthened by the hydrogen bonding, so that the structure of each compound is maintained in solution. It is suggested that this hydrogen bonding lowers the redox potentials of the Ru(II) centers due to polarization of the coordinated amide C=O bond, in which the oxygen atom becomes more electrostatically negative and its electron-donating ability is strengthened. The N-H protons in the coordinated amide moieties were found to undergo a reversible deprotonation-protonation process, and the redox potentials of the Ru(II) centers could be regulated in the range of 500 mV in CH(3)CN solutions. The Pourbaix diagram for 1 clearly showed that this proton-coupled redox behavior is a one-electron/one-proton process, and the pK(a) value was estimated to be approximately 6.

On the Mössbauer Spectra of IsopenicillinNSynthase and a Model {FeNO}7(S=3/2) System

We have carried out a series of density functional theory (DFT) calculations to predict the 57Fe Mössbauer quadrupole splittings (DeltaEQ) and isomer shifts (deltaFe) for the nitrosyl complex of isopenicillin N synthase with the substrate delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-valine (IPNS.ACV.NO) and an {FeNO}7 (S = 3/2) model system, FeL(NO)(N3)2 (L = N,N',N' '-trimethyl-1,4,7-triazacyclononane). B3LYP predictions on the model compound are in almost exact agreement with experiment. The same DFT methods did not enable the prediction of the experimental DeltaEQ and deltaFe results for IPNS.ACV.NO when using the experimental protein crystal structure but did permit good predictions of DeltaEQ, deltaFe, and the asymmetry parameter (eta) when using a fully optimized structure. This optimized structure also enabled good predictions of the Mössbauer spectra of the photodissociation product of IPNS.ACV.NO. Mulliken and natural bonding orbital (NBO) spin density analyses indicate an electronic configuration of FeII (S = 2) anti-ferromagnetically coupled to NO (S = 1/2) in the protein as well as in the model system and the geometry optimized structure helps explain part of the enzyme reaction.

The crystal structures of Zea mays and Arabidopsis 4-hydroxyphenylpyruvate dioxygenase

The transformation of 4-hydroxyphenylpyruvate to homogentisate, catalyzed by 4-hydroxyphenylpyruvate dioxygenase (HPPD), plays an important role in degrading aromatic amino acids. As the reaction product homogentisate serves as aromatic precursor for prenylquinone synthesis in plants, the enzyme is an interesting target for herbicides. In this study we report the first x-ray structures of the plant HPPDs of Zea mays and Arabidopsis in their substrate-free form at 2.0 A and 3.0 A resolution, respectively. Previous biochemical characterizations have demonstrated that eukaryotic enzymes behave as homodimers in contrast to prokaryotic HPPDs, which are homotetramers. Plant and bacterial enzymes share the overall fold but use orthogonal surfaces for oligomerization. In addition, comparison of both structures provides direct evidence that the C-terminal helix gates substrate access to the active site around a nonheme ferrous iron center. In the Z. mays HPPD structure this helix packs into the active site, sequestering it completely from the solvent. In contrast, in the Arabidopsis structure this helix tilted by about 60 degrees into the solvent and leaves the active site fully accessible. By elucidating the structure of plant HPPD enzymes we aim to provide a structural basis for the development of new herbicides.

Iron(II) Carboxylate Complexes Based on a Tetraimidazole Ligand as Models of the Photosynthetic Non-Heme Ferrous Sites: Synthesis, Crystal Structure, and Mössbauer and Magnetic Studies

The preparations, X-ray structures, and detailed physical characterization are presented for new complexes involving an iron(II) center, a tetraimidazole ligand (TIM), and different carboxylates. [Fe(TIM)(C(6)H(5)CH(2)CO(2))](ClO(4)) (1) crystallizes in the Pbca space group with a = 10.8947(13), b = 20.343(2), and c = 22.833(3) A, Z = 8, and V = 5060.6(11) A(3). [Fe(TIM)(CH(3)CO(2))](ClO(4)) (2) crystallizes in the Ia space group with a = 17.117(2), b = 10.3358(12), and c = 25.658(3) A, beta = 90.301(13) degrees, Z = 8, and V = 4539.5(9) A(3). In both structures, the iron(II) is hexacoordinated to the four N(imidazole) donors of the TIM ligand and the two O donors of a bidentate carboxylate. The flexibility of the carboxylate bidentate coordination, symmetrical or more or less asymmetrical, associated with the steric demand of the TIM ligand results in a remarkable versatility of the Fe(II)N(4)O(2) coordination geometry. The diversity in carboxylate bidentate coordination modes has allowed us to clearly show the importance of the structural and electronic effects, through IR and Mössbauer spectroscopy, of this apparently tenuous carboxylate shift. Comparison of the structural and Mössbauer properties of these complexes with the non-heme ferrous site of photosynthetic systems (i) shows that the metric parameters of site 2b, including the symmetrically chelated bidentate carboxylate, are closer to those of the non-heme ferrous site in the bacterial reaction centers of Rhodopseudomonas viridis and R. sphaeroides and (ii) suggests that the ligand environment of the non-heme ferrous center of PS 2 is close to the axially distorted octahedral symmetry resulting from an asymmetrical bidentate coordination of the -CO(2) motif, as in complex 1.

Mechanistic studies of 1-aminocyclopropane-1-carboxylic acid oxidase: single turnover reaction

The final step in the biosynthesis of the plant hormone ethylene is catalyzed by the non-heme iron-containing enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACCO). ACC is oxidized at the expense of O(2) to yield ethylene, HCN, CO(2), and two waters. Continuous turnover of ACCO requires the presence of ascorbate and HCO(3)(-) (or an alternative form), but the roles played by these reagents, the order of substrate addition, and the mechanism of oxygen activation are controversial. Here these issues are addressed by development of the first functional single turnover system for ACCO. It is shown that 0.35 mol ethylene/mol Fe(II)ACCO is produced when the enzyme is combined with ACC and O(2) in the presence of HCO(3)(-) but in the absence of ascorbate. Thus, ascorbate is not required for O(2) activation or product formation. Little product is observed in the absence of HCO(3)(-), demonstrating the essential role of this reagent. By monitoring the EPR spectrum of the sample during single turnover, it is shown that the active site Fe(II) oxidizes to Fe(III) during the single turnover. This suggests that the electrons needed for catalysis can be derived from a fraction of the initial Fe(II)ACCO instead of ascorbate. Addition of ascorbate at 10% of its K(m) value significantly accelerates both iron oxidation and ethylene formation, suggesting a novel high-affinity effector role for this reagent. This role can be partially mimicked by a non-redox-active ascorbate analog. A mechanism is proposed that begins with ACC and O(2) binding, iron oxidation, and one-electron reduction to form a peroxy intermediate. Breakdown of this intermediate, perhaps by HCO(3)(-)-mediated proton transfer, is proposed to yield a high-valent iron species, which is the true oxidizing reagent for the bound ACC.

Kinetic analysis of human homogentisate 1,2-dioxygenase

Homogentisate 1,2-dioxygenase (HGD) is a mononuclear Fe(II)-dependent oxygenase that catalyzes the third step in the pathway for the catabolism of tyrosine, the conversion of homogentisate (HG) to maleylacetoacetate (MAA). We have heterologously expressed and purified native human HGD in the apo form. Steady-state analysis varying the concentration of both HG and molecular oxygen shows that the purified enzyme has a turnover number of 16 s(-1). Our data suggest that HG binds to the apo-enzyme and that the apo-HGD.HG complex does not bind Fe(II) and dissociates slowly at approximately 0.028 s(-1). The rate constant for the dissociation of Fe(II) from the holo-enzyme as measured under anaerobic conditions is 0.00004 s(-1) and indicates that this process is not relevant in steady-state turnover. The addition of HG and molecular oxygen to the holo-enzyme is formally random as the holo-enzyme reduces molecular oxygen at a rate of 1.35x10(3) M(-1) s(-1) at 4 degrees C. The term ordered with respect to the addition of substrates is most descriptive as the rate of reduction of molecular oxygen must increase in the presence of HG to sustain the observed turnover number.

Bis(pyrazol-1-yl)acetates as Tripodal Heteroscorpionate Ligands in Iron Chemistry: Syntheses and Structures of Iron(II) and Iron(III) Complexes with bpza, bdmpza, and bdtbpza Ligands

The molecular structure of the previously reported species "[Fe(bdtbpza)Cl]" has been revealed by X-ray structure determination to be a ferrous dimer [Fe(bdtbpza)Cl](2) (2c) [bdtbpza = bis(3,5-di-tert-butylpyrazol-1-yl)acetate]. The syntheses of ferrous 2:1 complexes [Fe(bpza)(2)] (3a) and [Fe(bdtbpza)(2)] (3c) as well as ferric 1:1 complexes [NEt(4)][Fe(bpza)Cl(3)] (4a) and [NEt(4)][Fe(bdmpza)Cl(3)] (4b) [bpza = bis(pyrazol-1-yl)acetate, bdmpza = bis(3,5-dimethylpyrazol-1-yl)acetate] are reported. Complexes 3a, previously reported [Fe(bdmpza)(2)] (3b), and 3c are high-spin. No spin crossover to the low-spin state was observed in the temperature range of 5-350 K. 4a and 4b are synthesized in one step and in high yield from [NEt(4)](2)[Cl(3)FeOFeCl(3)]. 4a and 4b are iron(III) high-spin complexes. Crystallographic information: 2c (C(24)H(39)ClFeN(4)O(2).CH(2)Cl(2).CH(3)CN) is triclinic, P1, a = 12.171(16) A, b = 12.851(14) A, c = 13.390(13) A, alpha = 98.61(9) degrees, beta = 113.51(11) degrees, gamma = 108.10(5) degrees, Z = 2; 3a (C(8)H(7)Fe(0.5)N(4)O(2)) is monoclinic, P2(1)/n, a = 7.4784(19) A, b = 7.604(3) A, c = 16.196(4) A, beta = 95.397(9) degrees, Z = 4; 3c (C(24)H(39)Fe(0.5)N(4)O(2)) is monoclinic, P2(1)/n, a = 9.939(6) A, b = 18.161(10) A, c = 13.722(8) A, beta = 97.67(7) degrees, Z = 4; 4b (C(20)H(35)Cl(3)FeN(5)O(2)) is monoclinic, C2/c, a = 30.45(6) A, b = 12.33(2) A, c = 16.17(3) A, beta = 118.47(5) degrees, Z = 8.

Catalysis, evolution and life

Living organisms are unique in their ability to generate and replicate ordered systems from disordered components. Generation of order, replication of the individual, and evolution of the species all depend on the successful utilization of external energy derived from chemicals and light. The information for reproduction is encoded in nucleic acids, but evolution depends on a limited variability in replication, and proceeds through the selection of individuals with altered biochemistry. Essentially all biochemistry is catalyzed; therefore, altered biochemistry implies altered or new catalysts. In that sense catalysis is the medium of evolution. We propose that a basic property of enzymes, at least as fundamental as reaction rate enhancement, is to adjust the reaction path by altering and eventually optimizing the reversible interchange of chemical, electrical and mechanical energy among themselves and their reactants.