HAI YANG (US)
US20140053287A1 | 2014-02-20 |
HARA ET AL.: "A chemoenzymatic process for amide bond formation by an adenylating enzyme- mediated mechanism", NATURE, vol. 8, no. 1, 13 February 2018 (2018-02-13), pages 2950, XP055807422
DATABASE Protein [online] 13 February 2019 (2019-02-13), "RecName: Full=Tryptophan N-acetyltransferase ivoA; AltName: Full=Ivory mutation-related protein A; AltName: Full=Nonribosomal peptide synthetase ivoA; Short=NRPS ivoA", XP055807427, retrieved from ncbi Database accession no. C8V7P4
SAMPATH ET AL.: "Biochemical Characterization of Hpa2 and Hpa3, Two Small Closely Related Acetyltransferases from Saccharomyces cerevisiae", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 288, no. 30, 26 July 2013 (2013-07-26), pages 21506 - 21513, XP055807437
CLAIMS 1. A method of making a D-tryptophan or a substituted D-tryptophan analog comprising: combining L- tryptophan or a substituted L-tryptophan analog with a single-module nonribosomal peptide synthase ivoA polypeptide such that the IvoA polypeptide catalyzes: unidirectional stereoconversion of the L- tryptophan to a D-tryptophan; or unidirectional stereoconversion of the substituted L-tryptophan analog to a substituted D-tryptophan analog; so that the D-tryptophan or the substituted D-tryptophan analog is made. 2. The method of claim 1, wherein at least 90% of the L- tryptophan or substituted L-tryptophan analog combined in the method is converted to D-tryptophan or a substituted D-tryptophan analog. 3. The method of claim 1, wherein the method makes a substituted D-tryptophan analog. 4. The method of claim 3, wherein the substituted D-tryptophan analog comprises a 5-OMe-L-tryptophan, a 4-F-L-tryptophan, a 5-F-L-tryptophan, a 6-F-L- tryptophan, a 5-Cl-L-tryptophan, a 6-Cl-L-tryptophan, a 5-Br-L-tryptophan, a 4-Me- L-tryptophan, a 5-Me-L-tryptophan, a 6-Me-L-tryptophan, or a 7-Me-L-tryptophan. 5. The method of claim 1, wherein the single-module nonribosomal peptide synthase ivoA polypeptide comprises an amino acid sequence having at least a 90% identity to SEQ ID NO:1. 6. The method of claim 5, wherein the D-tryptophan or the substituted D- tryptophan is made via fermentation in a yeast strain selected to overexpress IvoA polypeptide. 7. The method of claim 6, further wherein the yeast strain: comprises an Aspergillus nidulans phosphopantetheinyl transferase gene; comprises a mutated histone acetyltransferase hpa3 gene; and/or comprises a heterologous leu2 gene. 8. The method of claim 7, wherein the yeast strain produces at least 1 mg/L of D- tryptophan or substituted D-tryptophan analog. 9. A system for generating a D-tryptophan or a substituted D-tryptophan analog comprising: a first container comprising a single-module nonribosomal peptide synthase ivoA polypeptide or a polynucleotide encoding a single-module nonribosomal peptide synthase ivoA polypeptide; and a second container comprising a buffer and/or a solution comprising an ATP. 10. The system of claim 9, wherein the system comprises a yeast strain that overexpresses a heterologous IvoA polypeptide having at least a 90% identity to SEQ ID NO: 1. 11. A composition of matter comprising: a single-module nonribosomal peptide synthase ivoA polypeptide comprising an amino acid sequence having at least a 90% identity to SEQ ID NO:1; L- tryptophan and D-tryptophan; or a substituted L-tryptophan analog and a substituted D-tryptophan analog. 12. The composition of claim 11, further comprising Saccharomyces Cerevisiae comprising an exogenous nucleic acid encoding the single-module nonribosomal peptide synthase ivoA polypeptide comprising an amino acid sequence having at least a 90% identity to SEQ ID NO:1. 13. The composition of claim 11, further comprising Saccharomyces Cerevisiae selected to: comprise a mutated histone acetyltransferase hpa3 gene; and/or comprise a heterologous leu2 gene. 14. The composition of claim 11, wherein the composition comprises L- tryptophan and D-tryptophan. 15. The composition of claim 11, wherein the composition comprises a substituted D-tryptophan analog. 16. The composition of claim 15, wherein the composition comprises a substituted D-tryptophan having an electron-withdrawing group or an electron donating group at position 4,5,6 or 7 on the tryptophan indole ring moiety. 17. The composition of claim 16, wherein the substituted D-tryptophan analog is selected from the group consisting of a 5-OMe-L-tryptophan, a 4-F-L-tryptophan, a 5- F-L-tryptophan, a 6-F-L-tryptophan, a 5-Cl-L-tryptophan, a 6-Cl-L-tryptophan, a 5- Br-L-tryptophan, a 4-Me-L-tryptophan, a 5-Me-L-tryptophan, a 6-Me-L-tryptophan, or a 7-Me-L-tryptophan. 18. The composition of claim 11, wherein the composition is a liquid and the D- tryptophan or the substituted D-tryptophan analog is present in the composition in amounts of at least 1 mg/L. 19. The composition of claim 18, wherein liquid is a yeast culture medium. 20. The composition of claim 11, wherein the composition is disposed in a vessel. |
Distinct from common PLP-dependent or PLP-independent amino acid racemases (Scheme 1), which often catalyze bidirectional stereoinversion and also inevitably lead to racemization (equilibrium constant approaches unity) (17), IvoA catalyzes unidirectional stereoinversion, completely converting L-tryptophan to its enantiomer D-tryptophan. The complete conversion is driven by coupled ATP hydrolysis, which is thermodynamically favored (Scheme 1) (18), and is enabled by the thiotemplate enzymology of IvoA (Figure 3). We reason that the activated tryptophan is delivered to the E domain as tryptophanyl-S-Ppant thioester, which undergoes epimerization to give a mixture of D/L-tryptophanyl-S-Ppant diastereoisomers in equilibrium. We propose that dynamic kinetic resolution may be accomplished by the C domain in a releasing step, which stereoselectively hydrolyzes the D-tryptophanyl-S-Ppant thioester to achieve irreversible conversion. As mentioned earlier, even though IvoA A domain prefers L-tryptophan, D- tryptophan can still be adenylated and thioesterified (Figure 9). In addition, the loaded D-tryptophanyl-S-Ppant underwent epimerization by IvoA E domain as evidenced by similar, yet slower deuterium “wash-in” behavior under multiple-turnover condition (Figure 15). The slower turnover measured by deuterium incorporation reflects the lower adenylation efficiency of D-tryptophan. Nonetheless, the occurrence of hydrogen-deuterium exchange at D-tryptophanyl-S-Ppant CĮ position not only suggests that epimerization is faster than the C-domain catalyzed D-specific tryptophanyl thioester hydrolysis, but also indicates that the D/L-tryptophanyl-S- Ppant equilibrium can be approached from either direction (Figure 3). However, IvoA cannot convert D-tryptophan to L-tryptophan, which suggests that the L-tryptophanyl- S-Ppant is not hydrolyzed by the C domain. A D-specific hydrolytic releasing C domain is therefore the key for unidirectional complete stereoinversion. To directly demonstrate the stereoselectivity of IvoA C domain, we purified the standalone IvoA-C and assayed its activity in vitro. Addition of IvoA-C in equimolar to either IvoA(Cº) mutant or IvoA-ǻC truncation mutant successfully rescued the impaired stereoinversion activity, which proved that the stand alone IvoA- C is active (Figure 16). We then synthesized both D- and L-tryptophanyl-S-N- acetylcysteamine as surrogate substrates mimicking the IvoA T domain bound tryptophanyl-S-Ppant intermediates. However, the enzyme did not catalyze hydrolysis significantly above the background nonenzymatic rate (Figure 17). Using D- tryptophanyl-S-pantetheine (D-Trp-pant) also did not improve enzymatic hydrolysis. We reason that the protein:protein interaction between T and C domain is important for substrate recognition, which has been shown in other studies of C domains (19). Hence, we chose to enzymatically load D/L-tryptophan to IvoA-ǻC(Eº) by taking advantage of the promiscuous A domain. It is imperative to inactivate the E domain in this truncation mutant in order to minimize the epimerization. The formation of corresponding D/L-tryptophanyl-S-Ppant of IvoA-ǻC was confirmed by intact protein mass spectrometry (Figure 18). Free excess D/L-tryptophan substrates were quickly removed from IvoA-ǻC(Eº) by using desalting spin columns and the loaded D/L- tryptophanyl-S-IvoA-ǻC(Eº) were immediately subjected to IvoA-C catalyzed hydrolysis. The liberated free tryptophan was then quantified by LC-MS. As shown in Figure 4, IvoA-C stereoselectively hydrolyzed D-tryptophanyl-S-IvoA-ǻC(Eº) over L-tryptophanyl-S-IvoA-ǻC(Eº). NRPS C domains that have thioesterase activity are rare, and to date only one example from crocacin PKS-NRPS hybrid assembly-line was known, but did not show stereoselectivity (20). Therefore, the IvoA-C characterized here represents a novel C domain and we classify it as a D CH2O subtype according to the universally acknowledged nomenclature (12). The verified stereoinversion activity of IvoA prompted us to explore its biocatalytic potential. D-tryptophan and its substituted analogues are important building blocks for many peptide pharmaceuticals, such as FDA approved lanreotide, pasireotide, octreotide, macimorelin, triptorelin, etc. Recently, there is growing interest in developing biocatalytic processes for syntheses of substituted D- tryptophans by stereoinversion and deracemization from the L-enantiomers and rac- tryptophans, respectively (21). However, to overcome the entropically unfavorable deracemization process (DGº = 0.4 kcal/mol) (22), the current methods are based on multi-step cascade reactions to establish non-equilibrium conditions for enrichment of D-enantiomers (21). In contrast, IvoA offers a concise one-step, direct nonredox stereoinversion/deracemization process, and allows us to access a library of D- tryptophan analogues in high enantiomeric excess (ee >99%) at millimolar level. Different substitution groups, either electron-withdrawing or electron-donating, at most positions (e.g. positions 4, 5, 6 and 7) on the indole ring can be tolerated (Table 2). No conversion of 2-Me-DL-tryptophan is due to inefficient activation by A domain (Figure 19), which suggests that substitution at 2-position may interfere with substrate recognition. The poor substrates are generally those with larger substituents (e.g. 5-NO 2 , 5-CN, 6-Br, 7-Br), which reflects the size limit by IvoA A domain. In light of recent success in A domain engineering (23), it is conceivable that the substrate scope can be expanded in the future by enlarging the substrate binding pocket of A domain. In summary, our biochemical study uncovered the unusual activity of IvoA, and our findings expand the function diversity of single-module NRPSs. The reassigned function of IvoA also provides insight to fungal pigment biosynthesis. By inverting the chirality of tryptophan, IvoA perhaps can modulate amino acid flux to pigment biosynthesis in vivo. Considering the proposed role of IvoB and IvoC, one can speculate that the D-configuration generated by IvoA may be retained in the final uncharacterized conidiophore pigment. Table 2. Biocatalytic stereoinversion or deracemization of substituted
1 . Materials and Methods 1 .1. Chemicals and general methods L-Tryptophan is purchased from Fisher Chemicals. D-Tryptophan is purchased from Acros Organics. N-acetyl-L-tryptophan and N-acetyl-D-tryptophan are purchased from TCI. NĮ-Boc-L-tryptophan-N-hydroxy-succinimide ester, NĮ-Boc- D-tryptophan-N-hydroxy-succinimide ester, and all other tryptophan amino acid derivatives are purchased from Chem-Impex Int’l. Inc. Isopropyl-ȕ-D-1-thio- galactopyranoside (IPTG) was purchased from Carbosynth. Tris-(2-carboxyethyl) phosphine hydrochloride (TCEP-HCl) was purchased from GoldBio Biotechnology. All other chemicals were purchased from Sigma-Aldrich. PCR reactions were performed using the Phusion® high-fidelity DNA polymerase (New England Biolabs) and used according to the manufacturer’s instructions. Custom oligonucleotides were synthesized by Integrated DNA Technologies. Escherichia coli strain DH10B was used for cloning procedures. 1 .2. Protein expression and purification The ivoA gene (AN10576) exon fragments were cloned from the genomic DNA extract of A. nidulans ǻEM strain (1. Liu, N.; Hung, Y.-S.; Gao, S.-S.; Hang, L.; Zou, Y.; Chooi, Y.-H.; Tang, Y. Identification and heterologous production of a benzoyl-primed tricarboxylic acid polyketide intermediate from the zaragozic acid a biosynthetic pathway. Org. Lett. 201719, 3560-3563), and assembled through yeast homologous recombination using a Frozen-EZ Yeast Transformation II Kit (Zymo research). Gene fragments were integrated into a 2m-based yeast expression vector (pXW55) with uracil auxotrophic marker and ADH2 promoter and terminator. To facilitate purification, the target gene was fused with an octahistidine tag at its N- terminus. The full-length wild-type IvoA and mutants were expressed in S. cerevisiae JHY686 strain and expression was autoinduced in YPD medium. Briefly, single colonies of yeast cells harboring plasmids was inoculated into SDCt uracil drop-out culture and left grown at 28 °C for 2 days. The seed culture was then inoculated into YPD culture (1 ml to 50 mL) and left grown at 28 °C for another 2 days. Cells were harvested by centrifugation and washed once with cell lysis buffer (50 mM K2HPO4 (pH 7.5), 10 mM imidazole, 300 mM NaCl, 5% glycerol). Cells were flash frozen in liquid nitrogen and lysed by using a stainless-steel Waring blender. The cell lysate was cleared by centrifugation at 26,000 g for 60 min at 4 °C and the supernatant was filtered through a 0.22 mm filter (Millipore). The filtrate was incubated with Ni 2+ - NTA resin for 30 min at 4 °C and then the slurry was loaded onto a gravity column. The resin was washed and eluted with increasing concentrations of imidazole in cell lysis buffer. The fractions were examined by SDS-PAGE gels and targeted proteins were subject to size-exclusion chromatography by using a HiLoad Superdex 200 26/60 column (GE Healthcare) equilibrated in storage buffer (50 mM K2HPO4 (pH 7.5), 150 mM NaCl, 1 mM TCEP). Pure fractions were concentrated to 20 mg/mL by Amicon concentrators (Millipore), supplemented with 10% glycerol and stored at -80 °C. Protein concentrations were determined by Bradford assay. For individual domain expression, the expression plasmids were constructed by subcloning the corresponding domain region into a modified pET28a (+) vector (Addgene plasmid #29656). The resulting N-terminal TEV protease cleavable hexahistidine tagged individual domains were overexpressed in E. coli BL21(DE3) cells in LB medium in the presence of 50 mg/L kanamycin. Expression was induced by 100 mM IPTG when OD600 reached 1.0 and the cell cultures were left grown at 16 °C overnight. Cells were harvested by centrifugation and lysed by sonication. Purification was performed similarly to the full-length protein. 1.3. Fermentation product isolation and purification The fermentation product was analyzed with a Shimadzu 2020 LC-MS (Phenomenex Kinetex, 1.7 mm, 2.0 X 100 mm, C18 column) using positive and negative mode electrospray ionization with a linear gradient of 5-95% MeCN-H 2 O supplemented with 0.1% (v/v) formic acid in 15 min followed by 95% MeCN for 3 min with a flow rate of 0.3 mL/min. For structural characterization, N-acetyl-D- tryptophan and D-tryptophan were isolated from a 2L yeast culture overexpressing IvoA protein. The cell pellets containing D-tryptophan were removed by centrifugation and the supernatant containing N-acetyl-D-tryptophan was collected separately. To purify N-acetyl-D-tryptophan, the pH value of the supernatant was adjusted to 3 by using 1M HCl. The acidified supernatant was extracted with ethyl acetate and the organic layer was combined. The organic solvent was removed by rotavap and the crude extract was dried over Na 2 SO 4 . N-Acetyl-D-tryptophan was purified by silica- gel chromatography. Fractions containing the target compound were combined and further purified by semipreparative HPLC using a reverse-phase column (Phenomenex Kinetics, C18, 5 mm, 100 Å, 250 x 4.6 mm). The planar structure of N- acetyl-D-tryptophan was confirmed by comparing NMR spectrum with spectrum reported in the literature and database. 3 1 H-NMR (500 MHz, CD 3 OD): 1.89 (s, 3H), 3.15 (dd, J = 14.7, 7.5 Hz, 1H), 3.35 (dd, overlap with solvent, 1H), 4.69 (t, J = 14.7, Hz, 1H), 7.00 (ddd, J = 8.0, 7.0, 1.0 Hz, 1H), 7.07 (m, 2H), 7.31 (dt, J = 8.1, 0.9 Hz, 1H), 7.56 (dt, J = 7.9, 1.0 Hz, 1H). The stereochemistry of N-acetyl-D-tryptophan was determined by chiral analytical HPLC with a CHIRALPAK® IA-3 (150 x 4.6 mm, 3 mm) at room temperature. The mobile phase was 80/20/0.1/0.1 hexanes/ethanol/TFA/DEA and the flow-rate was 1.0 mL/min. To purify D-tryptophan, the cell pellet was extracted by acetone and the solvent was removed by rotavap. The crude residue was dissolved in mobile phase A (water containing 0.1 (v/v) TFA) and applied to reverse-phase flash-chromatography. Basically, 20 mL of Cosmosil 140 C 18 -OPN resin (Nacalai Tesque, Inc.) was packed in a Luer-Lock, non-jacketed glass column (Sigma) and equilibrated with mobile phase A. The resin was washed with 3 column volume (CV) of mobile phase and then eluted with increasing methanol content in a step-wise manner. Tryptophan was eluted at 15-25% (v/v) methanol fractions. The pooled fractions were further purified by semipreparative HPLC using a reverse-phase column (Phenomenex Kinetics, C18, 5 mm, 100 Å, 250 x 4.6 mm). The planar structure of D-tryptophan was confirmed by comparing NMR spectrum with spectrum reported in the literature and database. 1 H- NMR (500 MHz, D2O): ^ 3.37 (dd, J = 15.4, 7.8 Hz, 1H), 3.51 (dd, J = 15.4, 5.0 Hz, 1H), 4.19 (dd, J = 7.7, 5.0 Hz, 1H), 7.20 (ddd, J = 8.0, 7.0, 1.1 Hz, 1H), 7.28 (ddd, J = 8.2, 7.0, 1.2 Hz, 1H), 7.32 (s, 1H), 7.54 (dt, J = 8.2, 1.0 Hz, 1H), 7.72(dt, J = 8.0, 1.0 Hz, 1H). Similarly, L-tryptophan was purified from yeast cells without overexpressing ivoA protein. 1 H-NMR (500 MHz, D2O): 3.40 (dd, J = 15.4, 7.6 Hz, 1H), 3.52 (dd, J = 15.4, 5.2 Hz, 1H), 4.26 (dd, J = 7.5, 5.0 Hz, 1H), 7.19 (t, J = 7.5 Hz, 1H), 7.28 (t, J = 7.6 Hz, 1H), 7.33 (s, 1H), 7.53 (d, J = 8.1 Hz, 1H), 7.71(d, J = 8.1 Hz, 1H). The stereochemistry was determined by chiral analytical HPLC with a Crownpak® CR(+) column (150 mm x 4 mm x 3.5 mm, Daicel) at room temperature. The mobile phase was aq. HClO 4 1% (w/v) supplemented with 15% (v/v) MeOH and the flow rate was 1.0 ml/min.
1.4. Enzymatic assay. The hydroxylamine-based colorimetric assay for adenylation activity was performed according to the literature (Kadi, N.; Challis, G. L. Chapter 17. Siderophore biosynthesis a substrate specificity assay for nonribosomal peptide synthetase-independent siderophore synthetases involving trapping of acyl-adenylate intermediates with hydroxylamine. Methods Enzymol. 2009, 458, 431-457). Acetyltryptophan acetyltransferase activity was performed by incubating 1-100 mM IvoA with 1 mM D-tryptophan or other substrates with 1 mM acetyl-CoA or 1 mM acetyl-phosphate in 100 mM phosphate buffer (pH 7.5). The reaction mixture was incubated at room temperature and the reaction was quenched at different time interval by mixing with 5-fold volume of methanol. The mixture was clarified by centrifugation to remove protein and salts, and the supernatant was dried in vaccuo by using speedvac. The residue was dissolved in methanol and subjected to LC-MS analysis. For ATP-dependent acetyltransferase activity, 1 mM L/D-tryptophan, 5 mM ATP, 1 mM CoA and 5 mM MgCl 2 were used. The ATP-dependent stereoinversion activity was typically performed with 2-5 mM IvoA, 1 mM L/D-tryptophan, 3 mM ATP and 10 mM MgCl 2 in 100 mM phosphate buffer (pH 7.5), and the reaction was quenched by mixing with 5-volume of methanol. The solvent was removed in vaccuo by speedvac and the residue was dissolved in ethanol and analyzed by chiral-HPLC by using a Crownpak® CR(+) column (150 mm x 4 mm x 3.5 mm, Daicel) at room temperature. The mobile phase was aq. HClO41% (w/v) supplemented with 15% (v/v) MeOH and the flow rate was 1.0 ml/min. When assays were performed in D2O, enzyme stock solution was buffer exchanged into K 2 HPO 4 buffer in D 2 O (pD 7.5) by using Zeba TM Spin Desalting Column (ThermoFisher Scientific). All substrates and cofactors were dissolved in the same buffer. The L-/D-tryptophan loading reactions were performed by incubating 80 mM holo-IvoA-ǻC with 5 mM ATP, 10 mM MgCl2 and 1 mM L-/D-tryptophan in a final volume of 50 mL. The reaction was allowed to proceed for 15 min before a two-fold dilution with mQH2O and analysis by UHPLC-ESI-Q-TOF-MS. The thioesterase activity assay of standalone IvoA-C was performed in ammonium acetate buffer (20 mM, pH = 6.9). Typically, 5 mM synthetic substrate (5% DMSO) was incubated with 50 mM enzyme. The reaction was analyzed by HPLC. Boiled enzyme was used as control to measure the background nonenzymatic hydrolysis. The loaded IvoA-ǻC(Eº) was prepared enzymatically by incubating holo- enzyme with respective substrate (1 mM) in the presence of excess ATP (5 mM) and MgCl2 (10 mM) in storage buffer for 2 min. The reaction was quenched by desalting the enzyme through Zeba TM Spin Desalting Column, which is equilibrated in the ammonium acetate buffer (20 mM, pH = 6.9). The desalted enzyme was immediately mixed with IvoA-C (50 mM), or boiled enzyme, or chemical hydrolysis (1 M KOH). The hydrolysis reaction was quenched after 1 min by mixing with 2 volume of acetonitrile and subjected to LC-MS analysis. 1.5. UHPLC-ESI-Q-TOF-MS Analysis of Intact Proteins The L-/D-tryptophan loading reactions were analyzed on a Bruker MaXis II ESI-Q-TOF-MS connected to a Dionex 3000 RS UHPLC fitted with an ACE C4-300 RP column (100 x 2.1 mm, 5 ^m, 30 °C). The column was eluted with a linear gradient of 5–100% MeCN containing 0.1% formic acid over 30 min. The mass spectrometer was operated in positive ion mode with a scan range of 200–3000 m/z. Source conditions were: end plate offset at í500 V; capillary at í4500 V; nebulizer gas (N2) at 1.8 bar; dry gas (N2) at 9.0 L min í1 ; dry temperature at 200 °C. Ion transfer conditions were: ion funnel RF at 400 Vpp; multiple RF at 200 Vpp; quadrupole low mass at 200 m/z; collision energy at 8.0 eV; collision RF at 2000 Vpp; transfer time at 110.0 ms; pre-pulse storage time at 10.0 ms. 1.6. Genetic manipulation The S. cerevisiae hpa3ǻ mutant strain derived from parent JHY686 strain was constructed by integration of a LEU2 marker to the hpa3 loci through homologous recombination. The correct integration was selected by colony-PCR. The resulting strain JHY686-YH (MATĮ lys2ǻ0 his3D1 leu2D0 ura3D0 pep4D SAL1 + HAP1 + CAT5(91M) MIP1(661T) MKT1(30G) RME1 (INS-308A) TAO3 (1493Q) prb1ǻADH2p-npgA-ACS1t hpa3ǻ LEU2) was used to transform plasmid overexpressing IvoA protein. 1.6 Synthesis of D-Trp-SNAC NĮ-Boc-D-tryptophan-N-hydroxy-succinimide ester (0.2 g, 0.5 mmol) was dissolved in anhydrous dichloromethane (10 mL) at room temperature, and to this solution was added N-acetylcysteamine (0.07 g, 0.6 mmol) and diisopropylethylamine (DIPEA, 0.12 g, 1 mmol). This was stirred at room temperature for 2 hrs and washed with saturated ammonium chloride. The organic layer was dried over sodium sulfate and removed by rotavap. The residue was subjected to silica flash chromatography. The resulting white solid product was dissolved in 2 mL of cocktail of 90% trifluoroacetic acid (TFA)/5% water/5% triisopropylsilane (TIPS) and stirred for 8 hrs. The solvents were evaporated to give a crude oil, which was taken up in minimal volume of dichloromethane and precipitated with diethyl ether. The resulting solid was further washed with diethyl ether to afford the final product in 80% yield. 1 H- NMR (d6-DMSO, 500 MHz): 11.12 (s, 1H), 8.56 (s, 3H), 8.06 (t, 1H, J = 5.3 Hz), 7.55 (d, 1H, J = 7.7 Hz), 7.38 (d, 1H, J = 8.1 Hz), 7.25 (d, 1H, J = 2.5 Hz), 7.10 (ddd, 1H, J = 8.2, 7.0, 1.2 Hz), 7.02 (ddd, 1H, J = 8.0, 7.0, 1.1 Hz), 4.45 (t, 1H, J = 6.6 Hz), 3.27 (m, 2H), 3.15 (q, 2H, J = 6.6 Hz), 2.96 (td, 2H, J = 6.8, 3.0 Hz), 1.79 (s, 3H). 13 C-NMR (d6-DMSO, 125 MHz): ^ 196.5, 169.4, 136.3, 127.0, 125.2, 121.3, 118.7, 118.1, 111.7, 106.2, 59.0, 37.8, 28.4, 27.6, 22.6. HRMS ESI m/z calculated for C15H20N3O2S + (M+H) + 306.1271, found 306.1258. 1.7 Synthesis of L-Trp-SNAC The synthesis of L-Trp-SNAC is essentially the same as D-Trp-SNAC, except N^-Boc-L-tryptophan-N-hydroxy-succinimide ester was used. 1 H-NMR (d6-DMSO, 500 MHz): ^ 11.14 (s, 1H), 8.61 (s, 3H), 8.06 (t, 1H, J = 6.2 Hz), 7.55 (d, 1H, J = 8.0 Hz), 7.38 (d, 1H, J = 8.1 Hz), 7.25 (s, 1H), 7.10 (t, 1H, J = 7.5 Hz), 7.02 (t, 1H, J = 7.5, 7.0, 1.1 Hz), 4.44 (t, 1H, J = 4.7 Hz), 3.28 (m, 2H), 3.14 (m, 2H), 2.96 (td, 6.7, 2.7, 2H), 1.80 (s, 3H). 13 C-NMR (d6-DMSO, 125 MHz): 196.5, 169.5, 136.3, 127.0, 125.2, 121.3, 118.7, 118.1, 111.7, 106.2, 59.0, 37.8, 28.4, 27.6, 22.6. HRMS ESI m/z calculated for C15H20N3O2S + (M+H) + 306.1271, found 306.1264. 1.8 Synthesis of D-Trp-pant NĮ-Boc-D-tryptophan-N-hydroxy-succinimide ester (0.1 g, 0.25 mmol) was dissolved in anhydrous dichloromethane (5 mL) at room temperature, and to this solution was added dimethyl ketal protected pantetheine prepared (80 mg, 0.25 mmol) 3 and DIPEA, 0.06 g, 0.5 mmol). This was stirred at room temperature for 2 hrs and washed with saturated ammonium chloride. The organic layer was dried over sodium sulfate and removed by rotavap. The residue was subjected to silica flash chromatography. The resulting white-yellow solid was dissolved in 5 mL of cocktail of 75% trifluoroacetic acid (TFA)/20% water/5% triisopropylsilane (TIPS) and stirred for 24 hrs. The solvents were evaporated to give a crude oil, which was taken up in minimal volume of dichloromethane and precipitated with diethyl ether. The resulting solid was further washed with diethyl ether to afford the final product in total 60% yield. 1 H-NMR (d6-DMSO, 500 MHz): 11.11 (s, 1H), 8.53 (s, 3H), 8.10 (t, 1H, J = 5.7 Hz), 7.72 (t, 1H, J = 6.1 Hz), 7.55 (d, 1H, J = 7.9 Hz), 7.38 (d, 1H, J = 8.1 Hz), 7.25 (d, 1H, J = 2.4 Hz), 7.10 (t, 1H, J = 7.5 Hz), 7.02 (t, 1H, J = 7.4 Hz), 4.45 (t, 1H, J = 6.7 Hz), 3.70 (s, 1H), 3.31 (m, overlap, 1H), 3.30 (m, overlap, 1H), 3.29 (m, 2H), 3.26 (m, 2H), 3.22 (m, overlap, 1H), 3.18 (m, overlap, 1H), 3.16 (m, 2H), 2.96 (m, 2H), 2.26 (t, 1H, J = 8.6 Hz), 0.80 (s, 3H), 0.78 (s, 3H). 13 C-NMR (d 6 -DMSO, 125 MHz): 196.5, 172.9, 170.7, 136.3, 126.9, 125.2, 121.3, 118.7, 118.1, 111.6, 106.1, 75.0, 68.0, 59.0, 39.1, 37.7, 35.2, f35.1, 34.8, 28.3, 21.0, 20.3 HRMS ESI m/z calculated for C22H33N4O5S+ (M+H)+ 465.2166, found 465.2193. Experimental procedures, chromatograms, and spectroscopic data can be found in U.S. Provisional Patent Application Serial No 62/902,527 filed on September 18, 2019 and Hai et al. J. Am. Chem. Soc. 2019, 141, 41, 16222, the contents of which are incorporated by reference. The invention disclosed herein has a number of embodiments. Embodiments of the invention include methods of making a D-tryptophan or a substituted D- tryptophan analog. These methods typically comprise combining L- tryptophan or a substituted L-tryptophan analog with a single-module nonribosomal peptide synthase ivoA polypeptide such that the IvoA polypeptide catalyzes: unidirectional stereoconversion of the L- tryptophan to a D-tryptophan; and/or unidirectional stereoconversion of the substituted L-tryptophan analog to a substituted D-tryptophan analog; so that the D-tryptophan or the substituted D-tryptophan analog is made. In certain embodiments of the invention, the single-module nonribosomal peptide synthase ivoA polypeptide comprises an amino acid sequence having at least a 90% identity to SEQ ID NO:1. As used herein, “Single-module nonribosomal peptide synthetase IvoA polypeptide” refers to both genetically engineered and naturally occurring enzymes including A. nidulans IvoA polypeptide and enzymes that are related to A. nidulans IvoA polypeptide in sequence but containing amino acid differences. D-tryptophan, for example, can be produced from naturally occurring enzymes that are similar to A. nidulans IvoA polypeptide (see, e.g. SEQ ID NO: 1 or SEQ ID NO: 2). It is known in the art that mutants can be created by standard molecular biology techniques to produce, for example, mutants of SEQ ID NO: 1 that improve catalytic efficiencies or the like. Typically such mutants will have a 50%-99% sequence similarity to SEQ ID NO: 1. In this context, the term “IvoA homologous enzyme” includes a IvoA polypeptide having at least 80%, 85%, 90%, 95%, 97%, 98% or 99% sequence identity with the amino acid sequence set out in SEQ ID NO: 1, wherein the polypeptide has the ability to convert L-tryptophan to D- tryptophan. Such mutants are readily made and then identified in assays which observe the production of a desired compound such as D-tryptophan (typically using A. nidulans IvoA polypeptide (e.g. SEQ ID NO: 1) as a control). These mutants can be used by the methods of this invention to make D-tryptophan or substituted D- tryptophans, for example. Such variants include, for instance, IvoA polypeptides wherein one or more amino acid residues in SEQ ID NO:1 are substituted, added, or deleted. In some embodiments of the invention, the methodology makes a D- tryptophan. In other embodiments of the invention, the methodology makes a substituted D-tryptophan analog. In certain embodiments of the invention, the substituted D-tryptophan analog comprises a 5-OMe-L-tryptophan, a 4-F-L- tryptophan, a 5-F-L-tryptophan, a 6-F-L-tryptophan, a 5-Cl-L-tryptophan, a 6-Cl-L- tryptophan, a 5-Br-L-tryptophan, a 4-Me-L-tryptophan, a 5-Me-L-tryptophan, a 6-Me- L-tryptophan, or a 7-Me-L-tryptophan. In illustrative methods of the invention, the method produces the D-tryptophan or D-tryptophan analog in significant enantiomeric excess, for example where at least 60%-90% of the L- tryptophan or substituted L- tryptophan analog combined in the method is converted to D-tryptophan or a substituted D-tryptophan analog. In embodiments of the invention, IvoA polypeptides of the invention can be expressed in a heterologous host, for example a heterologous bacteria, yeast or mammalian cell. Polynucleotides encoding such IvoA polypeptides for use in such embodiments can be those known to be present in Aspergillus nidulans (See, e.g. Aspergillus nidulans NT_107011.1 and AN 4641.2) and/or may be modified or synthesized polynucleotides, for example codon optimized polynucleotides useful in a heterologous host (see, e.g. U.S. Patent Publication Nos. 20080154027 and 20110124074 which are incorporated herein by reference). In illustrative methodological embodiments of the invention that are disclosed herein, the D- tryptophan or the substituted D-tryptophan is made via fermentation in a yeast strain selected to overexpress IvoA polypeptide. Optionally, the yeast strain comprises an Aspergillus nidulans phosphopantetheinyl transferase gene; comprises a mutated histone acetyltransferase hpa3 gene; and/or comprises a heterologous leu2 gene. Typically, the yeast strain used in the method produces at least 1 mg/L, 5 mg/L or 10 mg/L of D-tryptophan or substituted D-tryptophan analog. Embodiments of the invention also include compositions of matter. For example, one embodiment of the invention is a composition of matter comprising a single-module nonribosomal peptide synthase ivoA polypeptide comprising an amino acid sequence having at least a 90% identity to SEQ ID NO:1; and L- tryptophan and D-tryptophan (e.g. where an amount of L-tryptophan in the composition has been converted to D-tryptophan by the single-module nonribosomal peptide synthase ivoA polypeptide); or a L-tryptophan analog and a substituted D-tryptophan analog (e.g. where an amount of the substituted L-tryptophan analog in the composition has been converted to the corresponding substituted D-tryptophan analog by the single-module nonribosomal peptide synthase ivoA polypeptide). In some embodiments, the composition comprises L- tryptophan and D-tryptophan. In other embodiments, the composition comprises a substituted D-tryptophan analog. Optionally, for example, the composition comprises a substituted D-tryptophan having an electron- withdrawing group or an electron donating group at position 4,5,6 or 7 on the tryptophan indole ring moiety. In certain embodiments of the invention, the substituted D-tryptophan analog is selected from the group consisting of a 5-OMe-L- tryptophan, a 4-F-L-tryptophan, a 5-F-L-tryptophan, a 6-F-L-tryptophan, a 5-Cl-L- tryptophan, a 6-Cl-L-tryptophan, a 5-Br-L-tryptophan, a 4-Me-L-tryptophan, a 5-Me- L-tryptophan, a 6-Me-L-tryptophan, or a 7-Me-L-tryptophan. In some embodiments of the invention, the composition comprises a yeast such as Saccharomyces Cerevisiae or the like that comprises an exogenous nucleic acid encoding the single-module nonribosomal peptide synthase ivoA polypeptide comprising an amino acid sequence having at least a 90% identity to SEQ ID NO:1. Optionally, the composition comprises Saccharomyces Cerevisiae selected to comprise a mutated histone acetyltransferase hpa3 gene; and/or comprise a heterologous leu2 gene. In certain embodiments of the invention, the composition is a liquid (e.g. a yeast culture medium) and the D-tryptophan or the substituted D- tryptophan analog is present in the composition in amounts of at least 1, 5 or 10 mg/L. Typically, the composition is disposed in a vessel. Embodiments of the invention further include systems or kits for generating a D-tryptophan or a substituted D-tryptophan analog. Typically these systems or kits comprise a first container comprising a single-module nonribosomal peptide synthase ivoA polypeptide or a polynucleotide encoding a single-module nonribosomal peptide synthase ivoA polypeptide; and a second container comprising a buffer and/or a solution comprising an ATP. In certain embodiments of the invention, the system or kit comprises a yeast strain that overexpresses a heterologous IvoA polypeptide having at least a 90% identity to SEQ ID NO: 1. NRPS IvoA Sequences 1. Aspergillus nidulans 1704 amino acid wild type. ACCESSION C8V7P4, Galagan et al., Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438 (7071), 1105-1115 (2005). K
2. Aspergillus nidulans variant having a histidine tag.
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