Characterization of SpnQ from the spinosyn biosynthetic pathway of Saccharopolyspora spinosa: mechanistic and evolutionary implications for C-3 deoxygenation in deoxysugar biosynthesis

The C-3 deoxygenation step in the biosynthesis of d-forosamine (4-N,N-dimethylamino-2,3,4,6-tetradeoxy-d-threo-hexopyranose), a constituent of spinosyn produced by Saccharopolyspora spinosa, was investigated. The spnQ gene, proposed to encode a TDP-4-keto-2,6-dideoxy-d-glucose 3-dehydratase was cloned and overexpressed in E. coli. Characterization of the purified enzyme established that it is a PMP and iron-sulfur containing enzyme which catalyzes the C-3 deoxygenation in a reductase-dependent manner similar to that of the previously well characterized hexose 3-dehydrase E1 from Yersinia pseudotuberculosis. However, unlike E1, which has evolved to work with a specific reductase partner present in its gene cluster, SpnQ lacks a specific reductase, and works efficiently with general cellular reductases ferredoxin/ferredoxin reductase or flavodoxin/flavodoxin reductase. SpnQ also catalyzes C-4 transamination in the absence of an electron transfer intermediary and in the presence of PLP and l-glutamate. Under the same conditions, both E1 and the related hexose 3-dehydrase, ColD, catalyze C-3 deoxygenation. Thus, SpnQ possesses important features which distinguish it from other well studied homologues, suggesting unique evolutionary pathways for each of the three hexose 3-dehydrases studied thus far.     

Characterization of protein encoded by spnR from the spinosyn gene cluster of Saccharopolyspora spinosa: mechanistic implications for forosamine biosynthesis

d-Forosamine is a 4-N,N-(dimethylamino)-2,3,4,6-tetradeoxy-alpha-d-threo-hexopyranose found in spinosyn produced by Saccharopolyspora spinosa. Studies of spinosyn biosynthesis in S. spinosa led to the isolation of the entire biosynthetic gene cluster. Heterologous expression of spnR, one putative gene in forosamine biosynthesis, in E. coli and purification of the SpnR protein identified it as an aminotransferase catalyzing the conversion of the 4-keto-2,3,6-trideoxy sugar intermediate to the corresponding 4-amino sugar product. Identification of SpnR function relied on the use of a stable TMP-phosphonate sugar in place of TDP-sugar substrate to determine the function of SpnR. This strategy may find general applicability for designing probes to study enzymes which catalyze the transformation of labile deoxysugar intermediates.     

Mechanistic studies of the radical S-adenosyl-L-methionine enzyme DesII: EPR characterization of a radical intermediate generated during its catalyzed dehydrogenation of TDP-D-quinovose

DesII, a radical S-adenosyl-l-methionine (SAM) enzyme from Streptomyces venezuelae, catalyzes the deamination of TDP-4-amino-4,6-dideoxy-D-glucose to TDP-3-keto-4,6-dideoxy-D-glucose in the desosamine biosynthetic pathway. DesII can also catalyze the dehydrogenation of TDP-D-quinovose to the corresponding 3-keto sugar. Similar to other radical SAM enzymes, DesII catalysis has been proposed to proceed via a radical mechanism. This hypothesis is now confirmed by EPR spectroscopy with the detection of a TDP-D-quinovose radical intermediate having a g-value of 2.0025 with hyperfine coupling to two spin 1/2 nuclei, each with a splitting constant of 33.6 G. A significant decrease in the EPR line width is observed when the radical is generated in reactions conducted in D(2)O versus H(2)O. These results are consistent with a C3 α-hydroxyalkyl radical in which the p-orbital harboring the unpaired electron spin at C3 is periplanar with the C-H bonds at both C2 and C4.     

Flavodoxin as an Electronic Donor in Photosynthetic Inorganic Nitrogen Assimilation by Iron-deficient Chlorella fusca Cells

Two ferredoxin-dependent enzymes involved in the photosynthetic assimilation of nitrogen, nitrite reductase (EC 1.7.7.1) and glutamate synthase (EC 1.4.7.1) from Chlorella fusca have been shown to use either ferredoxin or flavodoxin (from the same organism) as electron donor. Nitrite reductase showed K _m, values of 13.8 ± 0.9 μ M for ferredoxin and 30.4 ± 7.8 μ M for flavodoxin. Glutamate synthase exhibited a Km of 6.6 ± 1.2 μ M for ferredoxin compared to a calculated K _m of 22.4 ± 6.4 μ M for flavodoxin.     

Characterization and investigation of substrate specificity of the sugar aminotransferase WecE from E. coli K12

WecE gene, encoding a sugar aminotransferase (SAT), has been cloned from E. coli K12 and expressed in E. coli BL21 (DE3). The enzyme was purified and characterized. WecE used TDP-4-keto-6-deoxy-D-glucose (TDP-D-Glc4O) and L-glutamate as a good amino acceptor and donor, respectively, leading to the production of TDP-4-amino-4,6-dideoxy-D-galactose (TDP-Fuc4N), which was identified by NMR studies. WecE also showed a similar activity for TDP-4-keto 6-deoxy-D-mannose (TDP-D-Man4O), but no activity for GDP-4-keto-6-deoxy-D-mannose (GDP-D-Man4O), suggesting that the nucleotide moiety would become a key determinant to the substrate specificity of amine acceptor for the activity of the SAT. Multiple alignments showed that SATs have four highly conserved motifs located around the active site and could be divided into three subgroups (VIalpha, VIbeta, and VIgamma) that might be closely related with their substrate specificities.     

Characterization of the TDP-D-ravidosamine biosynthetic pathway: one-pot enzymatic synthesis of TDP-D-ravidosamine from thymidine-5-phosphate and glucose-1-phosphate

Ravidomycin V and related compounds, e.g., FE35A-B, exhibit potent anticancer activities against various cancer cell lines in the presence of visible light. The amino sugar moieties (D-ravidosamine and its analogues, respectively) in these molecules contribute to the higher potencies of ravidomycin and analogues when compared to closely related compounds with neutral or branched sugars. Within the ravidomycin V biosynthetic gene cluster, five putative genes encoding NDP-D-ravidosamine biosynthetic enzymes were identified. Through the activities of the isolated enzymes in vitro, it is demonstrated that ravD, ravE, ravIM, ravAMT and ravNMT encode TDP-D-glucose synthase, TDP-4-keto-6-deoxy-D-glucose-4,6-dehydratase, TDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase, TDP-3-keto-6-deoxy-D-galactose-3-aminotransferase, and TDP-3-amino-3,6-dideoxy-D-galactose-N,N-dimethyl-transferase, respectively. A protocol for a one-pot enzymatic synthesis of TDP-D-ravidosamine has been developed. The results presented here now set the stage to produce TDP-D-ravidosamine routinely for glycosylation studies.     

The biosynthesis of acarbose and validamycin

The studies reported here have established the biosynthetic origin of the mC7N units of acarbose and validamycin from sedo-heptulose 7-phosphate, and have identified 2-epi-5-epi-valiolone as the initial cyclization product. The deoxyhexose moiety of acarbose arises from glucose with deoxythymidyl-diphospho-4-keto-6-deoxy-D-glucose (dTDP-4-keto-6-deoxy-D-glucose) as a proximate intermediate. However, despite the identical origin of the aminocyclitol moieties in acarbose and validamycin A, the pathways of their formation seem to be substantially different. Validamycin A formation involves a number of discrete ketocyclitol intermediates, 5-epi-valiolone, valienone, and validone, whereas no free intermediates have been identified on the pathway from 2-epi-5-epi-valiolone to the pseudodisaccharide moiety of acarbose. The stage is now set for unraveling the mechanism or mechanisms by which the two components of the pseudodisaccharide moieties of acarbose and validamycin are uniquely coupled to each other via a nitrogen bridge.     

Mechanostability of the Single‐Electron‐Transfer Complexes of Anabaena Ferredoxin–NADP+ Reductase

The complexes formed between the flavoenzyme ferredoxin–NADP⁺ reductase (FNR; NADP⁺=nicotinamide adenine dinucleotide phosphate) and its redox protein partners, ferredoxin (Fd) and flavodoxin (Fld), have been analysed by using dynamic force spectroscopy through AFM. A strategy is developed to immobilise proteins on a substrate and AFM tip to optimise the recognition ability. The differences in the recognition efficiency regarding a random attachment procedure, together with nanomechanical results, show two binding models for these systems. The interaction of the reductase with the natural electron donor, Fd, is threefold stronger and its lifetime is longer and more specific than that with the substitute under iron‐deficient conditions, Fld. The higher bond probability and two possible dissociation pathways in Fld binding to FNR are probably due to the nature of this complex, which is closer to a dynamic ensemble model. This is in contrast with the one‐step dissociation kinetics that has been observed and a specific interaction described for the FNR:Fd complex.     

Characterization of Radical SAM Adenosylhopane Synthase,HpnH, which Catalyzes the 5′‐Deoxyadenosyl Radical Addition to Diploptene in the Biosynthesis of C35 Bacteriohopanepolyols

Adenosylhopane is a crucial intermediate in the biosynthesis of bacteriohopanepolyols, which are widespread prokaryotic membrane lipids. Herein, it is demonstrated that reconstituted HpnH, a putative radical S‐adenosyl‐l ‐methionine (SAM) enzyme, commonly encoded in the hopanoid biosynthetic gene cluster, converts diploptene into adenosylhopane in the presence of SAM, flavodoxin, flavodoxin reductase, and NADPH. NMR spectra of the enzymatic reaction product were identical to those of synthetic (22R)‐adenosylhopane, indicating that HpnH catalyzes stereoselective C?C formation between C29 of diploptene and C5′ of 5′‐deoxyadenosine. Further, the HpnH reaction in D₂O‐containing buffer revealed that a D atom was incorporated at the C22 position of adenosylhopane. Based on these results, we propose a radical addition reaction mechanism catalyzed by HpnH for the formation of the C₃₅ bacteriohopane skeleton.     

A short formal synthesis of squalamine from a microbial metabolite

A short formal synthesis of squalamine is described, utilizing the biotransformation product 2, which is available in one step from commercially available 3-keto-23,24-bisnorchol-4-en-22-ol (1). Regioselective C-22 oxidation and C-24 sulfation of the corresponding alcohols in the presence of a free C-7 alcohol make for an efficient preparation of squalamine intermediate 11.     

Characterization of Radical SAM Adenosylhopane Synthase,HpnH, which Catalyzes the 5′-Deoxyadenosyl Radical Addition to Diploptene in the Biosynthesis of C35 Bacteriohopanepolyols

Adenosylhopane is a crucial intermediate in the biosynthesis of bacteriohopanepolyols, which are widespread prokaryotic membrane lipids. Herein, it is demonstrated that reconstituted HpnH, a putative radical S-adenosyl-l -methionine (SAM) enzyme, commonly encoded in the hopanoid biosynthetic gene cluster, converts diploptene into adenosylhopane in the presence of SAM, flavodoxin, flavodoxin reductase, and NADPH. NMR spectra of the enzymatic reaction product were identical to those of synthetic (22R)-adenosylhopane, indicating that HpnH catalyzes stereoselective C−C formation between C29 of diploptene and C5′ of 5′-deoxyadenosine. Further, the HpnH reaction in D₂O-containing buffer revealed that a D atom was incorporated at the C22 position of adenosylhopane. Based on these results, we propose a radical addition reaction mechanism catalyzed by HpnH for the formation of the C₃₅ bacteriohopane skeleton.     

Characterization of chemically modified steroids for doping control purposes by electrospray ionization tandem mass spectrometry

The discovery of the designer steroid tetrahydrogestrinone (THG) in elite athletes' doping control samples in 2003 demonstrated the availability of steroid derivatives prepared solely for doping purposes. Modern mass spectrometers utilizing electrospray ionization and collisionally activated dissociation (CAD) of analytes allow the structural characterization of steroids and their derivatization sites by the elucidation of fragmentation behaviors. A total of 21 steroids comprising either a 4,9,11-triene, a 3-keto-4-ene or a 3-keto-1-ene nucleus were investigated regarding their dissociation pathways, deuterated analogues were synthesized and fragmentation routes were postulated, permitting the identification of steroidal structures and modifications. Compounds based on a 4,9,11-triene steroid with an ethyl residue at C-13 (gestrinone analogues) generate abundant fragment ions at m/z 241 and 199, whereas the substitution of the C-13 ethyl group by a methyl residue (trenbolone analogues) results in a shift of m/z 241 to 227. Substances related to testosterone with a 3-keto-4-ene structure give rise to abundant fragment ions at m/z 109 and 97 whereas steroids with a 3-keto-1-ene nucleus eliminate the A-ring including the carbons C-1-C-4, in addition to C-19 that is proposed to migrate from C-10 to C-1 under CAD conditions.     

In search of oligo(2-thienyl)-substituted pyridine derivatives: a modular approach to di-, tri- and tetra(2-thienyl)pyridines

Herein, we describe our attempts to systematically prepare a series of oligo(2-thienyl)-substituted pyridine derivatives. The crucial starting material, a β-alkoxy-β-ketoenamide, is easily available on a large scale by the reaction of lithiated methoxyallene with thiophene-2-carbonitrile and thiophene-2-carboxylic acid. This three-component reaction is followed by intramolecular cyclization to yield the suitably functionalized 2,6-di(2-thienyl)-substituted pyridine derivates. The two oxygen atoms allow the programmed activation of positions C-3, C-4, or C-5 of the pyridine ring to perform palladium-catalyzed coupling reactions with thiophene-2-boronic acid or 2-(tributylstannyl)thiophene, and alternatively, reductive removal of groups. With this concept, we were able to prepare five pyridine derivatives with 2-thienyl substituents in the 2,6-, 2,3,6-, 2,4,6-, 2,3,4,6-, and 2,3,5,6-positions. 2,3,4,5,6-Penta(2-thienyl)pyridine was not available with our methods. The UV/Vis and fluorescence spectra of all pyridines were recorded and showed a dependence on the substitution pattern and protonation state. For the protonated 2,3,5,6-tetra(2-thienyl)-substituted pyridine, a Stokes shift of about 180 nm with an emission at 515 nm was observed.     

LASER FLASH-INDUCED PHOTOREDUCTION OF PHOTOSYNTHETIC FERREDOXINS AND FLAVODOXIN BY 5-DEAZARIBOFLAVIN AND BY A

Abstract Laser flash photolysis has been used to compare the kinetics of reduction of ferredoxin isoforms from the green alga Monoraphidium braunii, and the ferredoxin and flavodoxin from the cyanobacterium Anabaena PCC 7119, by 5-deazariboflavin semiquinone (dRM) and the viologen analogue 1,l‘-propylene-2,2′-bipyridyI (PDQ ⁺). Similar ionic strength-independent second-order rate constants (1.4 × 10⁸M^?1 s ^?1) were obtained for the reduction of both algal ferredoxin isoforms by dRM For the reduction of oxidized flavodoxin by dRM, a more complex behavior was observed, with a second-order rate constant for dRM. decay of 1.8 × 10⁸M^?1 S^?1, and a first-order (i.e. protein concentration independent) rate constant of 450 s^?1, that probably corresponds to the protonation of the FMN semiquinone cofactor, which occurs subsequent to electron transfer. A value of 5 × 10⁷M^?1 S^?1 was obtained for the second-order rate constant of flavodoxin semiquinone reduction by dRM The reduction of ferredoxins and flavodoxin semiquinone by PDQ ⁺ showed nonlinear protein concentration dependencies, consistent with a minimal two-step mechanism involving complex formation followed by intracomplex electron transfer. A negative ionic strength effect on the kinetic constants was obtained, indicating the existence of attractive electrostatic interactions during electron transfer. With all the ferredoxins the k_∞ values (rate constants extrapolated to infinite ionic strength) for the second-order step of the reduction process (complex formation) are smaller than previously reported for spinach ferredoxin, although Anabaena ferredoxin is somewhat more reactive than are the algal ferredoxins with the viologen. In contrast, the k_∞ values for the first-order component of ferredoxin reduction (intracomplex electron transfer) for the algal ferredoxins are comparable to that for spinach ferredoxin, whereas for this reaction the ferredoxin from Anabaena has a smaller intrinsic reactivity. As compared with the ferredoxins, Anabaena flavodoxin has significantly smaller k_∞ values for its interaction with the viologen analogue, both for complex formation and for electron transfer. In all cases the existence of nonproductive electrostatic interactions between the viologen analogue and the proteins is suggested by the data.     

The biosynthesis of GDP-L-colitose: C-3 deoxygenation is catalyzed by a unique coenzyme B6-dependent enzyme

l-Colitose (1) is a 3,6-dideoxyhexose found in the O-antigen of gram-negative lipopoly-saccharides. While the biosynthesis of many deoxysugars have previously been investigated, l-colitose is distinct in that it originates from GDP-d-mannose. In contrast, other 3,6-dideoxyhexoses arise from CDP-d-glucose. Therefore, the enzymes involved in the l-colitose biosynthetic pathway must be specifically tailored to utilize such a modified substrate. The mode for deoxygenation at C-3 of colitose is of particular interest because this conversion in other naturally occurring 3,6-dideoxyhexoses requires a pair of enzymes, E1 and E3, acting in concert. Interestingly, no E3 equivalent was identified in the five open reading frames of the col biosynthetic gene cluster from Yersinia pseudotuberculosis IVA. However, the gene product of colD showed moderate similarity with the E1 gene (ddhC/ascC) of the ascarylose pathway (27% identity and 42% similarity). Because E1 is a pyridoxamine 5'-phosphate (PMP)-dependent enzyme, it was thought that ColD might also utilize PMP. Indeed, turnover was observed during incubation of ColD with substrate in the presence of excess PMP, but not with pyridoxal 5'-phosphate (PLP). However, the rate of product formation increased by more than 40-fold when l-glutamate was included in the PLP incubation. The formation of alpha-ketoglutarate as a byproduct under these conditions clearly indicated that ColD functions as a transaminase, recognizing both PMP and PLP. In this paper, we propose a novel biosynthetic route for colitose, including the unprecedented C-3 deoxygenation performed solely by ColD. The utilization of PMP in a dehydration reaction is rare, but the combined deoxygenation-transamination activity makes ColD a unique enzyme.     

Importance of specific hydrogen-bond donor-acceptor interactions for the key carbocycle-forming reaction catalyzed by 2-deoxy-scyllo-inosose synthase in the biosynthesis of 2-deoxystreptamine-containing aminocyclitol antibiotics

A crucial enzyme in the biosynthesis of the 2-deoxystreptamine aglycon of clinically important aminocyclitol antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which converts ubiquitous D-glucose 6-phosphate (G-6-P) into the specific carbocycle 2-deoxy-scyllo-inosose. Among all the oxygenated carbons of the substrate, C-1, -4, -5, and -6 are directly involved in the chemical transformation. To get insight into the roles of C-2 and C-3 hydroxy groups, 2-deoxy-2-fluoro-, 3-deoxy-3-fluoro-, 2-amino-2-deoxy-, and 3-amino-3-deoxy-D-glucose 6-phosphates (2-F-G-6-P, 3-F-G-6-P, 2-NH(2)-G-6-P, and 3-NH(2)-G-6-P, respectively) were subjected to the DOIS reaction as probe, since a fluorine substituent generally acts as a hydrogen-bond acceptor, and an ammonium functionality derived physiologically from an amino group as a hydrogen-bond donor. Among those tested, 2-F-G-6-P and 3-NH(2)-G-6-P were used as substrates by DOIS and were converted into the corresponding deoxyfluoro- and aminodeoxy-scyllo-inososes, respectively. In contrast, 3-F-G-6-P and 2-NH(2)-G-6-P were inactive in the cyclization reaction. Clearly, DOIS recognizes the G-6-P substrate through specific hydrogen-bonding interactions, i.e., through a hydrogen-donating group for C-2 and an accepting group for C-3 of the substrate. Modeling of DOIS based on the structure of evolutionary-related dehydroquinate synthase is also described.     

Rerouting nucleophilic substitution from the 4-position to the 2- or 6-position of 2,4-dihalopyridines and 2,4,6-trihalopyridines: the solution to a long-standing problem

2,4-Difluoro-, 2,4,6-trifluoro-, and 2,3,4,6-tetrafluoropyridine undergo nucleophilic substitution preferentially if not exclusively at the 4-position. However, after the introduction of a trialkylsilyl group at C-3 or C-5, the halogen at the 6-(2-)position is displaced selectively. This synthetically valuable regiocontrol can also be realized with other halopyridines such as 2,4-dichloro- and 2,4,6-trichloropyridine.     

Staurosporine and rebeccamycin aglycones are assembled by the oxidative action of StaP, StaC, and RebC on chromopyrrolic acid

In the biosynthesis of the antitumor indolocarbazoles rebeccamycin and staurosporine by streptomycetes, assembly of the aglycones involves a complex set of oxidative condensations. Overall formation of aglycones K252c and arcyriaflavin A from their biosynthetic precursor chromopyrrolic acid involves four- and eight-electron oxidations, respectively. This process is catalyzed by the remarkable enzyme StaP, with StaC and RebC acting to direct the level of oxidation in the newly formed five-membered ring. An aryl-aryl coupling reaction is integral to this transformation as well as oxidative decarboxylation of the dicarboxypyrrole moiety of chromopyrrolic acid. Herein we describe the heterologous expression of staP, staC, and rebC in Escherichia coli and the activity of the corresponding enzymes in constructing the two distinct six-ring scaffolds. StaP is a cytochrome P450 enzyme, requiring dioxygen, ferredoxin, flavodoxin NADP(+)-reductase, and NAD(P)H for activity. StaP on its own converts chromopyrrolic acid into three aglycone products, K252c, arcyriaflavin A, and 7-hydroxy-K252c; in the presence of StaC, K252c is the predominant product, while the presence of RebC directs formation of arcyriaflavin A. (18)O-Labeling studies indicate that the oxygen(s) of the pyrrolinone and maleimide functionalities of the aglycones formed are all derived from dioxygen. This work allowed for the in vitro reconstitution of the full biosynthetic pathway from l-tryptophan to the staurosporine and rebeccamycin aglycones, K252c and 1,11-dichloroarcyriaflavin A.     

Synthesis and biological evaluation of the first example of an eight-membered iminoalditol

The synthesis of the first examples of eight-membered iminoalditols has been achieved from 2,3,4,6-tetra-O-benzyl-d-glucopyranose by way of a ring-closing metathesis. The (2R,3R,4R,5S)-2-hydroxymethyl-azocane-3,4,5-triol (3a), which has the d-gluco configuration for C-2-C-5 and appears to exist predominantly in a boat-chair conformation, is a weak inhibitor of glycosidases.     

Synthese de derives de la purpurosamine C,composant de la gentamicine C1a

The synthesis of derivatives of purpurosaimine C and epi-purpurosamine C is described, from methyl 2,3,4,6-tetra-O?-methylsulphonyl-α-d-galacto and glucopyranosides 2 and 3 by reaction with azide ion to give diazides 4 and 5, transformed in a series of reactions via epoxides 6 and 7 into the corresponding olefines 16 and 17, thermal rearrangement to give diazides 18 and 19, which were transformed into the methyl glycosides 27 and 29 and mercaptolysis with ethanethiol followed by N-acetylation, gave 2,6-diacetamido-2,3,4,6-tetradeoxy-d-erythro-hexose diethyl dithioacetal 30 (identical with authentic 30 prepared from gentamicin C_1a)and 2,6-diacetamido-2,3,4,6-tetradeoxy-d- threo-hexose diethyl dithioacetal 31, an enantiomer of a mercaptolysis product of dihydrosisomicin.