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1.
Direct detection of thioester intermediate mixtures bound to EpoC, a 195 kDa polyketide synthase, has been achieved using limited proteolysis and Fourier-transform mass spectrometry (FTMS). Incubation with various N-acetylcysteamine thioester (S-NAC) substrate mimics produced mass shifts on the EpoC ACP domain consistent with their condensation with an enzyme-bound carbanion produced by the decarboxylation of methylmalonyl-S-EpoC. Reconstitution of EpoA-ACP, EpoB, and EpoC gave a +165.0 Da mass shift consistent with the formation of the methylthiazolyl-methacrylyl product by incorporation of acetyl-CoA, cysteine, and methylmalonyl-CoA. Thioester-templated reaction intermediates and products are typically characterized by quantifying radioactive substrates, either enzyme bound or chemically hydrolyzed. In contrast, the MS-based methodology described here provides semiquantifiable ratios of free enzyme, intermediate, and product occupancy and reveals that certain substrates result in a >50% formation of nonproductive intermediates.  相似文献   

2.
For the uninterrupted observation of natural product bioassembly on nonribosomal peptide synthetases, Quadrupole Fourier Transform Mass Spectrometry (Q-FTMS) was utilized to directly interrogate peptides harboring covalently modified residues in yersiniabactin synthetase. After proteolysis in CNBr, the peptides corresponding to each carrier site were identified and visualized using a continuous kinetic assay. Overall, complex intermediate formation was rapid, with observation of the HPTT-beta-keto-2,2-dimethyl-S-ACP intermediate within 4 s, while each active site reached saturation within approximately 20 s. Reduction of the beta-keto group at the ACP domain was found to have the slowest rate, accumulating only after 40 s. This represents the first study to correlate five active sites in tandem with kinetic and structural resolution of the complex intermediates in addition to regiospecific information preserved in the assay.  相似文献   

3.
Nonreducing iterative polyketide synthases (NR-PKSs) are responsible for assembling the core of fungal aromatic natural products with diverse biological properties. Despite recent advances in the field, many mechanistic details of polyketide assembly by these megasynthases remain unknown. To expand our understanding of substrate loading, polyketide elongation, cyclization, and product release, active site occupancy and product output were explored by Fourier transform mass spectrometry using the norsolorinic acid anthrone-producing polyketide synthase, PksA, from the aflatoxin biosynthetic pathway in Aspergillus parasiticus. Here we report the simultaneous observation of covalent intermediates from all catalytic domains of PksA from in vitro reconstitution reactions. The data provide snapshots of iterative catalysis and reveal an underappreciated editing function for the C-terminal thioesterase domain beyond its recently established synthetic role in Claisen/Dieckmann cyclization and product release. The specificity of thioesterase catalyzed hydrolysis was explored using biosynthetically relevant protein-bound and small molecule acyl substrates and demonstrated activity against hexanoyl and acetyl, but not malonyl. Processivity of polyketide extension was supported by the inability of a nonhydrolyzable malonyl analog to trap products of intermediate chain lengths and by the detection of only fully extended species observed covalently bound to, and as the predominant products released by, PksA. High occupancy of the malonyl transacylase domain and fast relative rate of malonyl transfer compared to starter unit transfer indicate that rapid loading of extension units onto the carrier domain facilitates efficient chain extension in a manner kinetically favorable to ultimate product formation.  相似文献   

4.
BACKGROUND: EntF is a 142 kDa four domain (condensation-adenylation-peptidyl carrier protein-thioesterase) nonribosomal peptide synthetase (NRPS) enzyme that assembles the Escherichia coli N-acyl-serine trilactone siderophore enterobactin from serine, dihydroxybenzoate (DHB) and ATP with three other enzymes (EntB, EntD and EntE). To assess how EntF forms three ester linkages and cyclotrimerizes the covalent acyl enzyme DHB-Ser-S-PCP (peptidyl carrier protein) intermediate, we mutated residues of the proposed catalytic Ser-His-Asp triad of the thioesterase (TE) domain. RESULTS: The Ser1138-->Cys mutant (kcat decreased 1000-fold compared with wild-type EntF) releases both enterobactin (75%) and linear (DHB-Ser)2 dimer (25%) as products. The His 1271-->Ala mutant (kcat decreased 10,000-fold compared with wild-type EntF) releases only enterobactin, but accumulates both DHB-Ser-O-TE and (DHB-Ser)2-O-TE acyl enzyme intermediates. Electrospray ionization and Fourier transform mass spectrometry of proteolytic digests were used to analyze the intermediates. CONCLUSIONS: These results establish that the TE domain of EntF is both a cyclotrimerizing lactone synthetase and an elongation catalyst for ester-bond formation between covalently tethered DHB-Ser moieties, a new function for chain-termination TE domains found at the carboxyl termini of multimodular NRPSs and polyketide synthases.  相似文献   

5.
BACKGROUND: Coumarin group antibiotics, such as novobiocin, coumermycin A1 and clorobiocin, are potent inhibitors of DNA gyrase. These antibiotics have been isolated from various Streptomyces species and all possess a 3-amino-4-hydroxy-coumarin moiety as their structural core. Prior labeling experiments on novobiocin established that the coumarin moiety was derived from L-tyrosine, probably via a beta-hydroxy-tyrosine (beta-OH-Tyr) intermediate. Recently the novobiocin gene cluster from Streptomyces spheroides was cloned and sequenced and allows analysis of the biosynthesis of the coumarin at the biochemical level using overexpressed and purified proteins. RESULTS: Two open reading frames (ORFs), NovH and NovI, from the novobiocin producer S. spheroides have been overexpressed in Escherichia coli, purified and characterized for tyrosine activation and oxygenation which are the initial steps in coumarin formation. The 65 kDa NovH has two predicted domains, an adenylation (A) and a peptidyl carrier protein (PCP), reminiscent of non-ribosomal peptide synthetases. Purified NovH catalyzes L-tyrosyl-AMP formation by its A domain, can be posttranslationally phosphopantetheinylated on the PCP domain, and accumulates the covalent L-tyrosyl-S-enzyme intermediate on the holo PCP domain. The second enzyme in the pathway, NovI, is a 45 kDa heme protein that functions as a cytochrome P450-type monooxygenase with specificity for the tyrosyl-S-NovH acyl enzyme. The product beta-OH-tyrosyl-S-NovH was detected by alkaline release and high performance liquid chromatography analysis of radioactive [3H]beta-OH-Tyr and by mass spectrometry. Also detected was 4-OH-benzaldehyde, a retro aldol breakdown product of beta-OH-Tyr. The amino acid released was (3R,2S)-3-OH-Tyr by comparison with authentic standards. CONCLUSIONS: This work establishes that NovH and NovI are responsible for the formation of a beta-OH-Tyr intermediate that is covalently tethered to NovH in novobiocin biosynthesis. Comparable A-PCP/P450 pairs for amino acid beta-hydroxylation are found in various biosynthetic gene clusters, such as ORF19/ORF20 in the chloroeremomycin cluster for tyrosine, CumC/CumD in the coumermycin A1 cluster for tyrosine, and NikP1/NikQ in the nikkomycin cluster for histidine. This phenomenon of covalent docking of the amino acid in a kinetically stable thioester linkage prior to chemical modification by downstream tailoring enzymes, could represent a common strategy for controlling the partitioning of the amino acid for incorporation into secondary metabolites.  相似文献   

6.
Many virulence factors and bioactive compounds with antifungal, antimicrobial, and antitumor properties are produced via the non-ribosomal peptide synthetase (NRPS) or polyketide synthase(PKS) paradigm. During the biosynthesis of these natural products, substrates, intermediates and side products are covalently tethered to the NRPS or PKS catalyst, introducing mass changes, making these biosynthetic systems ideal candidates for interrogation by large molecule mass spectrometry. This review serves as an introduction into the application of electrospray ionization Fourier-Transform massspectrometry (ESI-FTMS) to investigate NRPS and PKS systems. ESI-FTMS can be used to understand substrate tolerance, timing of covalent linkages, timing of tailoring reactions and the transfer of substrates and biosynthetic intermediates from domain to domain. Therefore we not only highlight key mechanistic insights for thiotemplate systems as found on the enterobactin,yersiniabactin, epothilone, clorobiocin, coumermycin, pyoluteorin, gramicidin, mycosubtilin, C-1027,6-deoxyerythronolide B and FK520 biosynthetic pathways, but we also explain the approaches taken to identify active sites from complex digests and compare the FTMS based assay to traditional assays and other mass spectrometric techniques. Although mass spectrometry was introduced over two decades ago to investigate NRPS and PKS biosynthetic systems, this is the first review devoted to this methodology.  相似文献   

7.
The nonribosomal peptide synthetases (NRPSs) are one of the most promising resources for the production of new bioactive molecules. The mechanism of NRPS catalysis is based around sequential catalytic domains: these are organized into modules, where each module selects, modifies, and incorporates an amino acid into the growing peptide. The intermediates formed during NRPS catalysis are delivered between enzyme centers by peptidyl carrier protein (PCP) domains, which makes PCP interactions and movements crucial to NRPS mechanism. PCP movement has been linked to the domain alternation cycle of adenylation (A) domains, and recent complete NRPS module structures provide support for this hypothesis. However, it appears as though the A domain alternation alone is insufficient to account for the complete NRPS catalytic cycle and that the loaded state of the PCP must also play a role in choreographing catalysis in these complex and fascinating molecular machines.  相似文献   

8.
Electrophilic allylic substitution of allylstannanes with aldehyde and imine substrates could be achieved by employment of palladium pincer complex catalysts. It was found that the catalytic activity of the pincer complexes is highly dependent on the ligand effects. The best results were obtained by employment of PCP pincer complexes with weakly coordinating counterions. In contrast to previous applications for electrophilic allylic substitutions via bisallylpalladium complexes, the presented reactions involve monoallylpalladium intermediates. Thus, employment of pincer complex catalysts extends the synthetic scope of the palladium-catalyzed allylic substitution reactions. Moreover, use of these catalysts eliminates the side reactions occurring in transformations via bisallylpalladium intermediates. The key intermediate of the electrophilic substitution reaction was observed by (1)H NMR spectroscopy. This intermediate was characterized as an eta(1)-allyl-coordinated pincer complex. Density functional theory (DFT) modeling shows that the electrophilic attack can be accomplished with a low activation barrier at the gamma-position of the eta(1)-allyl moiety. According to the DFT calculations, this reaction takes place via a six-membered cyclic transition-state (TS) structure, in which the tridentate coordination state of the pincer ligand is preserved. The stereoselectivity of the reaction could be explained on the basis of the six-membered cyclic TS model.  相似文献   

9.
The formation of methylenecyclopropanes by enzymatic desaturation of 11-cyclopropylundecanoic acid (1) and its disubstituted derivatives cis- and trans-3-5 has been investigated using the Delta(11) desaturase of Spodoptera littoralis as model enzyme. Gas chromatography coupled to mass spectrometry analyses of methanolyzed lipidic extracts from tissues incubated with each probe revealed that all the cyclopropyl fatty acids were transformed into the corresponding 11-cyclopropylidene acids, except for compound trans-5 (5b), which was not desaturated at C11. The formation of methylenecyclopropane 9 as the only reaction product from 1 indicates that a potential radical intermediate is too short-lived to allow rearrangement reactions. Information on the Delta(11) desaturase substrate binding domain is provided considering the cyclopropyl probes 3-5 as conformationally restricted analogues of the straight-chain substrates.  相似文献   

10.
The iminophosphorane Cl(3)P[double bond]NAr (1a, Ar = 2-fluorophenyl) reacts metathetically with imines at 80 degrees C to produce [double bond]NR exchange products. Compound 1a effectively catalyzes imine/imine and imine/carbodiimide cross-metathesis. The observation of [double bond]NR exchange products as well as spectroscopic evidence for the existence of diazaphosphetidine type intermediates suggests that a [2 + 2] addition/elimination mechanism is the primary pathway for substrates with N-alkyl substituents and a secondary pathway for N-aryl imines. In contrast to previously studied carbodiimide systems, the resting state of the catalyst is the iminophosphorane and not the diazaphosphetidine. For N-aryl imines, Lewis-acid catalysis appears to be the dominant mechanism, not addition/elimination. For N-alkyl imines, a decomposition pathway, involving HCl elimination from a phosphorus intermediate, is competitive in some cases.  相似文献   

11.
Type I modular polyketide synthases (PKSs), which are responsible for the biosynthesis of many biologically active agents, possess a ketosynthase (KS) domain within each module to catalyze chain elongation. Acylation of the KS active site Cys residue is followed by transfer to malonyl‐ACP to yield an extended β‐ketoacyl chain (ACP=acyl carrier protein). To date, the precise contribution of KS selectivity in controlling product fidelity has been unclear. Six KS domains from trans‐acyltransferase (trans‐AT) PKSs were subjected to a mass spectrometry based elongation assay, and higher substrate selectivity was identified for the elongating step than in preceding acylation. A close correspondence between the observed KS selectivity and that predicted by phylogenetic analysis was seen. These findings provide insights into the mechanism of KS selectivity in this important group of PKSs, can serve as guidance for engineering, and show that targeted mutagenesis can be used to expand the repertoire of acceptable substrates.  相似文献   

12.
L Du  B Shen 《Chemistry & biology》1999,6(8):507-517
BACKGROUND: Nonribosomal peptide synthetases (NRPSs) catalyze the assembly of a structurally diverse group of peptides by the multiple-carrier thiotemplate mechanism. All NRPSs known to date are exclusively type I modular enzymes that consist of domains, such as adenylation (A), peptidyl carrier protein (PCP) and condensation (C) domains, for individual enzyme activities. Although several A and PCP domains have been demonstrated to function independently, aminoacylation in trans has been successful only between PCPs and their cognate A domains. RESULTS: We have identified within the bleomycin-biosynthesis gene cluster from Streptomyces verticillus ATCC15003 the blmI gene that encodes a discrete PCP protein. We overexpressed the blmI gene in Escherichia coli, purified the BlmI protein, and demonstrated that apo-BlmI can be efficiently modified into holo-BlmI either in vivo or in vitro by PCP-specific 4'-phosphopantetheine transferases (PPTases). Unlike the PCP domains in type I NRPSs, BlmI lacks its cognate A domain and can be aminoacylated by Val-A, an A domain from a completely unrelated type I NRPS. CONCLUSIONS: BlmI represents the first characterized type II PCP. The BlmI type II PCP, like the PCP domains of type I NRPSs, can be 4'-phospho-pantetheinylated by PCP-specific PPTases but is biochemically distinct in that it can be aminoacylated by an A domain from a completely unrelated type I NRPS. Our results provide for the first time the genetic and biochemical evidence to support the existence of a type II NRPS, which might be useful in the combinatorial manipulation of NRPS proteins to generate novel peptides.  相似文献   

13.
Liu Y  Zheng T  Bruner SD 《Chemistry & biology》2011,18(11):1482-1488
Phosphopantetheine-modified carrier domains play a central role in the template-directed, biosynthesis of several classes of primary and secondary metabolites. Fatty acids, polyketides, and nonribosomal peptides are constructed on multidomain enzyme assemblies using phosphopantetheinyl thioester-linked carrier domains to traffic and activate building blocks. The carrier domain is a dynamic component of the process, shuttling pathway intermediates to sequential enzyme active sites. Here, we report an approach to structurally fix carrier domain/enzyme constructs suitable for X-ray crystallographic analysis. The structure of a two-domain construct of Escherichia coli EntF was determined with a conjugated phosphopantetheinyl-based inhibitor. The didomain structure is locked in an active orientation relevant to the chemistry of nonribosomal peptide biosynthesis. This structure provides details into the interaction of phosphopantetheine arm with the carrier domain and the active site of the thioesterase domain.  相似文献   

14.
钱荣  郭寅龙  吕龙 《中国化学》2009,27(1):123-129
更换底物保护基团的化学方法与质谱、同位素标记以及核磁方法联用表征钯催化的烯醇环化反应中间体。实验表明更换底物的保护基团方法可以明显降低反应速度,延长关键中间体离子的存活寿命,不仅清晰地观察了反应的整个进程而且成功地捕获检测表征了其中关键中间体离子。进一步,串联质谱(SORI-CAD)方法研究了其中一些中间体离子的气相裂解反应行为,归纳总结其气相裂解反应的途径。结合同位素标记的结构为它们结构的确证提供了丰富信息。  相似文献   

15.
Tellurium tetrachloride adds to alkynes via two pathways: a concerted syn-addition that yields Z-tri- and -tetrasubstituted alkenes or an anti-addition that yields E-alkenes. The mechanistic aspects of these divergent pathways for TeCl4 addition to alkynes have been investigated by on-line electrospray ionization (tandem) mass spectrometry (ESI-MS(/MS)). Via ESI-MS(/MS), we have been able to intercept and characterize the active electrophile TeCl3+ in tetrahydrofuran (THF) solutions of TeCl4, as well as its THF complex and several TeClx(OH)y+ derivatives. For the first time, also, key Te(IV) cationic intermediates of the electrophilic addition of TeCl4 to alkynes were captured for gas-phase MS investigation. The detailed structural data of cyclic tellurane intermediates intercepted herein seems to provide insights into the coordinative behavior of the Te(IV) atom and its mode of action towards biological targets.  相似文献   

16.
Alternating current (AC) electrolysis is an emerging field in synthetic chemistry, however its mechanistic studies are challenged by the effective characterization of the elusive intermediate processes. Herein, we develop an operando electrochemical mass spectrometry platform that allows time-resolved mapping of stepwise electrosynthetic reactive intermediates in both direct current and alternating current modes. By dissecting the key intermediate processes of electrochemical functionalization of arylamines, the unique reactivities of AC electrosynthesis, including minimizing the over-oxidation/reduction through the inverse process, and enabling effective reaction of short-lived intermediates generated by oxidation and reduction in paired electrolysis, were evidenced and verified. Notably, the controlled kinetics of reactive N-centered radical intermediates in multistep sequential AC electrosynthesis to minimize the competing reactions was discovered. Overall, this work provides direct evidence for the mechanism of AC electrolysis, and clarifies the underlying reasons for its high efficiency, which will benefit the rational design of AC electrosynthetic reactions.  相似文献   

17.
Studying the interplay between nonribosomal peptide synthetases (NRPS), a major source of secondary metabolites, and crucial external modifying enzymes is a challenging task since the interactions involved are often transient in nature. By applying a range of synthetic inhibitor‐type compounds, a stabilized complex appropriate for structural analysis was generated for such a tailoring enzyme and an NRPS domain. The complex studied comprises an NRPS peptidyl carrier protein (PCP) domain bound to the Cytochrome P450 enzyme that is crucial for the provision of β‐hydroxylated amino acid precursors in the biosynthesis of the cyclic depsipeptide skyllamycin. The structure reveals that complex formation is governed by hydrophobic interactions, the presence of which can be controlled through minor alterations in PCP structure that enable selectivity amongst multiple highly similar PCP domains.  相似文献   

18.
Mono- and dimethylation of hydroxylamine on nitrogen does not significantly affect rates of initial attack of NHMeOH and NMe(2)OH on bis(2,4-dinitrophenyl)phosphate (BDNPP), which is largely by oxygen phosphorylation. O-Methylation, however, blocks this reaction and NH(2)OMe then slowly reacts with BDNPP via N-attack at phosphorus and at the aryl group. With NHMeOH, the initial product of O-attack at phosphorus reacts further, either by reaction with a second NHMeOH or by a spontaneous shift of NHMe to the aryl group via a transient cyclic intermediate. There is a minor N-attack of NHMeOH on BDNPP in an S(N)2(Ar) reaction. Reactions occurring via N-attack are blocked by N-dimethylation, and reaction of NMe(2)OH with BDNPP occurs via O-attack, generating a long-lived product. Reaction mechanisms have been probed, and intermediates identified, by using both NMR and MS spectroscopy, with the novel interception of key reaction intermediates in the course of reaction by electrospray ionization mass and tandem mass spectrometry.  相似文献   

19.
An innovative technique to investigate the intermediates involved in the biosynthesis of the lipoheptapeptide surfactin from Bacillus subtilis OKB105 combining whole‐cell matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) with targeted generation of knock‐out mutants was demonstrated. This method allows efficient, sensitive detection of biosynthetic intermediates in a minimum of time directly at the outer surface of microbial cells picked from agar plates or in surface extracts prepared thereof. Biosynthesis of surfactin is encoded by the srf‐operon which is organized into four open reading frames which have been attributed to three multifunctional NRPS enzymes (SrfA‐C) and a thioesterase/acyltransferase enzyme SrfD. For the wild‐type strain OKB 105 only the end product surfactin was found mass spectrometrically. For the detection of lipopeptide intermediates three plasmid‐ and transposon‐insertion mutants were generated interrupting the surfactin assembly line at defined positions. Strain LAB 327 was mutated in the spacer region between enzymes SrfA and B. Here only SrfA was active with the lipotripeptide β‐OH‐acyl‐L‐Glu‐L‐Leu‐D‐Leu as the end product. Mutant OKB 120 bears a transposon mutation in SrfB between the first and second amino acid activating modules SrfB1 and SrfB2. It showed all intermediates from the lipodi‐ until to the lipotetrapeptide β‐OH‐acyl‐L‐Glu‐L‐Leu‐D‐Leu‐L‐Val. In LAB 223 SrfC was knocked out by a transposon mutation. It produced the lipohexapeptide β‐OH‐acyl‐L‐Glu‐L‐Leu‐D‐Leu‐L‐Val‐L‐Asp‐D‐Leu. Our work highlights the applicability and the potential of whole‐cell MALDI‐TOFMS as an innovative efficient tool for the analysis of intermediate steps of biosynthetic pathways. Copyright © 2009 John Wiley & Sons, Ltd.  相似文献   

20.
A new standard reference material (SRM) for drugs of abuse in human serum (SRM 1959) has been developed. This SRM is intended to be used as a control material for laboratories performing analysis of drugs of abuse in blood to evaluate the accuracy of their methods. SRM 1959 is a frozen human serum material fortified with seven compounds for which analyses are performed to determine evidence of illegal drug use: benzoylecgonine (BZE), methadone (METH), methamphetamine (MAMP), morphine (MOR), nordiazepam (NOR), phencyclidine (PCP), and 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid (THC-9-COOH). Two independent methods involving isotope dilution (ID)-gas chromatography/mass spectrometry (GC/MS) and ID-liquid chromatography/mass spectrometry (LC/MS) were used for the value assignment. For THC-9-COOH, an additional measurement using LC/tandem mass spectrometry (LC/MS/MS) was also included. All methods used isotopically labeled compounds as internal standards and solid-phase extractions to isolate the analytes from the serum. The GC/MS methods used different clean-up procedures from those used for the LC/MS-based methods. Repeatability with within-set coefficients of variation (CVs) ranged from 0.5% to 4.3% for the GC/MS methods and from 0.2% to 1.2% for the LC/MS-based methods. Intermediate precision with between-set CVs for all the methods ranged from 0.1% to 1.1%. Agreement between the GC/MS and LC/MS methods ranged from 0.8% to 8.8%. The results from the methods were combined to obtain the certified concentrations and their expanded uncertainties.  相似文献   

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