Substrate‐Tuned Catalysis of the Radical S‐Adenosyl‐L‐Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis

NosL is a radical S‐adenosyl‐L ‐methionine (SAM) enzyme that converts L ‐Trp to 3‐methyl‐2‐indolic acid, a key intermediate in the biosynthesis of a thiopeptide antibiotic nosiheptide. In this work we investigated NosL catalysis by using a series of Trp analogues as the molecular probes. Using a benzofuran substrate 2‐amino‐3‐(benzofuran‐3‐yl)propanoic acid (ABPA), we clearly demonstrated that the 5′‐deoxyadenosyl (dAdo) radical‐mediated hydrogen abstraction in NosL catalysis is not from the indole nitrogen but likely from the amino group of L ‐Trp. Unexpectedly, the major product of ABPA is a decarboxylated compound, indicating that NosL was transformed to a novel decarboxylase by an unnatural substrate. Furthermore, we showed that, for the first time to our knowledge, the dAdo radical‐mediated hydrogen abstraction can occur from an alcohol hydroxy group. Our study demonstrates the intriguing promiscuity of NosL catalysis and highlights the potential of engineering radical SAM enzymes for novel activities.     

Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues

Radical S‐adenosyl‐l ‐methionine (SAM) enzymes utilize a [4Fe‐4S] cluster to bind SAM and reductively cleave its carbon–sulfur bond to produce a highly reactive 5′‐deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical‐based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical‐based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside‐containing compounds by using radical SAM‐dependent reactions.     

Crystal Structure of Tryptophan Lyase (NosL): Evidence for Radical Formation at the Amino Group of Tryptophan

Streptomyces actuosus tryptophan lyase (NosL) is a radical SAM enzyme which catalyzes the synthesis of 3‐methyl‐2‐indolic acid, a precursor in the synthesis of the promising antibiotic nosiheptide. The reaction involves cleavage of the tryptophan Cα? Cβ bond and recombination of the amino‐acid‐derived ‐COOH fragment at the indole ring. Reported herein is the 1.8 Å resolution crystal structure of NosL complexed with its substrate. Unexpectedly, only one of the tryptophan amino hydrogen atoms is optimally placed for H abstraction by the SAM‐derived 5′‐deoxyadenosyl radical. This orientation, in turn, rules out the previously proposed delocalized indole radical as the species which undergoes Cα? Cβ bond cleavage. Instead, stereochemical considerations indicate that the reactive intermediate is a ^.NH tryptophanyl radical. A structure‐based amino acid sequence comparison of NosL with the tyrosine lyases ThiH and HydG strongly suggests that an equivalent ^.NH radical operates in the latter enzymes.     

Revisiting the Mechanism of the Anaerobic Coproporphyrinogen III Oxidase HemN

HemN is a radical S‐adenosyl‐l ‐methionine (SAM) enzyme that catalyzes the oxidative decarboxylation of coproporphyrinogen III to produce protoporphyrinogen IX, an intermediate in heme biosynthesis. HemN binds two SAM molecules in the active site, but how these two SAMs are utilized for the sequential decarboxylation of the two propionate groups of coproporphyrinogen III remains largely elusive. Provided here is evidence showing that in HemN catalysis a SAM serves as a hydrogen relay which mediates a radical‐based hydrogen transfer from the propionate to the 5′‐deoxyadenosyl (dAdo) radical generated from another SAM in the active site. Also observed was an unexpected shunt product resulting from trapping of the SAM‐based methylene radical by the vinyl moiety of the mono‐decarboxylated intermediate, harderoporphyrinogen. These results suggest a major revision of the HemN mechanism and reveal a new paradigm of the radical‐mediated hydrogen transfer in radical SAM enzymology.     

Sulfonium‐Based Homolytic Substitution Observed for the Radical SAM Enzyme HemN

Sulfur‐based homolytic substitution (S_H reaction) plays an important role in synthetic chemistry, yet whether such a reaction could occur on the positively charged sulfonium compounds remains unknown. In the study of the anaerobic coproporphyrinogen III oxidase HemN, a radical S‐adenosyl‐l ‐methionine (SAM) enzyme involved in heme biosynthesis, we observed the production of di‐(5′‐deoxyadenosyl)methylsulfonium, which supports a deoxyadenosyl (dAdo) radical‐mediated S_H reaction on the sulfonium center of SAM. The sulfonium‐based S_H reactions were then investigated in detail by density functional theory calculations and model reactions, which showed that this type of reactions is thermodynamically favorable and kinetically competent. These findings represent the first report of sulfonium‐based S_H reactions, which could be useful in synthetic chemistry. Our study also demonstrates the remarkable catalytic promiscuity of the radical SAM superfamily enzymes.     

The monohydrates of the four polar dipeptides l‐seryl‐l‐asparagine,l‐seryl‐l‐tyrosine,l‐tryptophanyl‐l‐serine and l‐tyrosyl‐l‐tryptophan

The crystal structures of the four dipeptides l ‐seryl‐l ‐asparagine monohydrate, C₇H₁₃N₃O₅·H₂O, l ‐seryl‐l ‐tyrosine monohydrate, C₁₂H₁₆N₂O₅·H₂O, l ‐tryptophanyl‐l ‐serine monohydrate, C₁₄H₁₇N₃O₄·H₂O, and l ‐tyrosyl‐l ‐tryptophan monohydrate, C₂₀H₂₁N₃O₄·H₂O, are dominated by extensive hydrogen‐bonding networks that include cocrystallized solvent water molecules. Side‐chain conformations are discussed on the basis of previous observations in dipeptides. These four dipeptide structures greatly expand our knowledge on dipeptides incorporating polar residues such as serine, asparagine, threonine, tyrosine and tryptophan.     

N‐Acetyl‐l‐tyrosine methyl ester monohydrate at 293 and 123 K

The crystal structure of a protected l ‐tyrosine, namely N‐acetyl‐l ‐tyrosine methyl ester monohydrate, C₁₂H₁₅NO₄·H₂O, was determined at both 293 (2) and 123 (2) K. The structure exhibits a network of O—H...O and N—H...O hydrogen bonds, in which the water molecule plays a crucial role as an acceptor of one and a donor of two hydrogen bonds. Molecules of water and of the protected l ‐tyrosine form hydrogen‐bonded layers perpendicular to [001]. C—H...π interactions are observed in the hydrophobic regions of the structure. The structure is similar to that of N‐acetyl‐l ‐tyrosine ethyl ester monohydrate [Soriano‐García (1993). Acta Cryst. C 49 , 96–97].     

Expanding the Chemistry of the Class C Radical SAM Methyltransferase NosN by Using an Allyl Analogue of SAM

The radical S‐adenosylmethionine (SAM) superfamily enzymes cleave SAM reductively to generate a highly reactive 5′‐deoxyadenosyl (dAdo) radical, which initiates remarkably diverse reactions. Unlike most radical SAM enzymes, the class C radical SAM methyltransferase NosN binds two SAMs in the active site, using one SAM to produce a dAdo radical and the second as a methyl donor. Here, we report a mechanistic investigation of NosN in which an allyl analogue of SAM (allyl‐SAM) was used. We show that NosN cleaves allyl‐SAM efficiently and the resulting dAdo radical can be captured by the olefin moieties of allyl‐SAM or 5′‐allylthioadenosine (ATA), the latter being a derivative of allyl‐SAM. Remarkably, we found that NosN produced two distinct sets of products in the presence and absence of the methyl acceptor substrate, thus suggesting substrate‐triggered production of ATA from allyl‐SAM. We also show that NosN produces S‐adenosylhomocysteine from 5′‐thioadenosine and homoserine lactone. These results support the idea that 5′‐methylthioadenosine is the direct methyl donor in NosN reactions, and demonstrate great potential to modulate radical SAM enzymes for novel catalytic activities.     

l‐Phenyl­alanyl‐l‐alanine dihydrate

A new type of molecular arrangement for dipeptides is observed in the crystal structure of l ‐phenyl­alanyl‐l ‐alanine dihydrate, C₁₂H₁₆N₂O₃·2H₂O. Two l ‐Phe and two l ‐Ala side chains aggregate into large hydro­phobic columns within a three‐dimensional hydrogen‐bond network.     

Determination of l‐tryptophan and l‐kynurenine derivatized with (R)‐4‐(3‐isothiocyanatopyrrolidin‐1‐yl)‐7‐(N,N‐dimethylaminosulfonyl)‐2,1,3‐benzoxadiazole by LC‐MS/MS on a triazole‐bonded column and their quantification in human serum

The concentrations of l ‐tryptophan (Trp) and the metabolite l ‐kynurenine (KYN) can be used to evaluate the in‐vivo activity of indoleamine 2,3‐dioxygenase (IDO) and tryptophan 2,3‐dioxygenase (TDO). As such, a novel method involving derivatization of l ‐Trp and l ‐KYN with (R)‐4‐(3‐isothiocyanatopyrrolidin‐1‐yl)‐7‐(N,N‐dimethylaminosulfonyl)‐2,1,3‐benzoxadiazole (DBD‐PyNCS) and separation by high‐performance liquid chromatography (HPLC) with tandem mass spectrometric (MS/MS) detection on a triazole‐bonded column (Cosmosil HILIC®) was developed to determine their concentrations. The optimized mobile phase, CH₃CN/10 mm ammonium formate in H₂O (pH 5.0) (90:10, v/v) eluted isocratically, resulted in satisfactory separation and MS/MS detection of the analytes. The detection limits of l ‐Trp and l ‐KYN were approximately 50 and 4.0 pm , respectively. The column temperature affected the retention behaviour of the Trp and KYN derivatives, with increased column temperatures leading to increased capacity factors; positive enthalpy changes were revealed by van't Hoff plot analyses. Using the proposed LC‐MS/MS method, l ‐Trp and l ‐KYN were successfully determined in 10 μL human serum using 1‐methyl‐l ‐Trp as an internal standard. The precision and recovery of l ‐Trp were in the ranges 2.85–9.29 and 95.8–113%, respectively, while those of l ‐KYN were 2.51–16.0 and 80.8–98.2%, respectively. The proposed LC‐MS/MS method will be useful for evaluating the in vivo activity of IDO or TDO. Copyright © 2016 John Wiley & Sons, Ltd.     

Phenyl‐ring rotational disorder in the two‐dimensional hydrogen‐bonded structure of the 1:1 proton‐transfer salt of the diazo‐dye precursor 4‐(phenyldiazenyl)aniline (aniline yellow) with l‐tartaric acid

In the structure of the 1:1 proton‐transfer compound from the reaction of l ‐tartaric acid with the azo‐dye precursor aniline yellow [4‐(phenyldiazenyl)aniline], namely 4‐(phenyldiazenyl)anilinium (2R,3R)‐3‐carboxy‐2,3‐dihydroxypropanoate, C₁₂H₁₂N₃⁺·C₄H₅O₆⁻, the asymmetric unit contains two independent 4‐(phenyldiazenyl)anilinium cations and two hydrogen l ‐tartrate anions. The structure is unusual in that all four phenyl rings of the two cations have identical rotational disorder with equal occupancy of the conformations. The two hydrogen l ‐tartrate anions form independent but similar chains through head‐to‐tail carboxyl–carboxylate O—H...O hydrogen bonds [graph set C(7)], which are then extended into a two‐dimensional hydrogen‐bonded sheet structure through hydroxy O—H...O hydrogen‐bonded links. The anilinium groups of the 4‐(phenyldiazenyl)anilinium cations are incorporated into the sheets and also provide internal hydrogen‐bonded extensions, while their aromatic tails are layered in the structure without significant association except for weak π–π interactions [minimum ring centroid separation = 3.844 (3) Å]. The hydrogen l ‐tartrate residues of both anions exhibit the common short intramolecular hydroxy–carboxylate O—H...O hydogen bonds. This work provides a solution to the unusual disorder problem inherent in the structure of this salt, as well as giving another example of the utility of the hydrogen tartrate anion in the generation of sheet substructures in molecular assembly processes.     

l‐Leucinium perchlorate

Crystals of l ‐leucinium perchlorate, C₆H₁₄NO₂⁺·ClO₄⁻, are built up from protonated l ‐leucinium cations and perchlorate anions. l ‐Leucinium cations related by a twofold screw axis are inter­connected by N—H⋯O hydrogen bonds into zigzag chains parallel to [010]. The O atoms of the perchlorate anions act as acceptors of hydrogen bonds that link the l ‐leucinium chains into separated but inter­acting two‐dimensional layers parallel to (001). Since the title compound crystallizes in a non‐centrosymmetric space group, it can be useful as a material for non‐linear optics. The efficiency of second harmonic generation is about twice that of K₂[HPO₄].     

Design of peptides with α,β‐de­hydro residues: pseudo‐tripeptide N‐benzyl­oxy­carbonyl–ΔLeu–l‐Ala–l‐Leu–OCH3

The title peptide N‐benzyl­oxy­carbonyl–ΔLeu–l ‐Ala–l ‐Leu–OCH₃ [methyl N‐(benzyl­oxy­carbonyl)‐α,β‐de­hydro­leucyl‐l ‐alanyl‐l ‐leucinate], C₂₄H₃₅N₃O₆, was synthesized in the solution phase. The peptide adopts a type II′β‐turn conformation which is stabilized by an intramolecular 4 1 N—H?O hydrogen bond. The crystal packing is stabilized by two intermolecular N—H?O hydrogen bonds.     

The Catalytic Mechanism of the Class C Radical S‐Adenosylmethionine Methyltransferase NosN

S ‐Adenosylmethionine (SAM) is one of the most common co‐substrates in enzyme‐catalyzed methylation reactions. Most SAM‐dependent reactions proceed through an S_N2 mechanism, whereas a subset of them involves radical intermediates for methylating non‐nucleophilic substrates. Herein, we report the characterization and mechanistic investigation of NosN, a class C radical SAM methyltransferase involved in the biosynthesis of the thiopeptide antibiotic nosiheptide. We show that, in contrast to all known SAM‐dependent methyltransferases, NosN does not produce S ‐adenosylhomocysteine (SAH) as a co‐product. Instead, NosN converts SAM into 5′‐methylthioadenosine as a direct methyl donor, employing a radical‐based mechanism for methylation and releasing 5′‐thioadenosine as a co‐product. A series of biochemical and computational studies allowed us to propose a comprehensive mechanism for NosN catalysis, which represents a new paradigm for enzyme‐catalyzed methylation reactions.     

Oriented (Local) Electric Fields Drive the Millionfold Enhancement of the H‐Abstraction Catalysis Observed for Synthetic Metalloenzyme Analogues

This contribution follows the recent remarkable catalysis observed by Groves et al. in hydrogen‐abstraction reactions by a) an oxoferryl porphyrin radical‐cation complex [Por^?+Fe^IV(O)L_ax] and b) a hydroxoiron porphyrazine ferric complex [PyPzFe^III(OH)L_ax], both of which involve positively charged substituents on the outer circumference of the respective macrocyclic ligands. These charge‐coronated complexes are analogues of the biologically important Compound I (Cpd I) and synthetic hydroxoferric species, respectively. We demonstrate that the observed enhancement of the H‐abstraction catalysis for these systems is a purely electrostatic effect, elicited by the local charges embedded on the peripheries of the respective macrocyclic ligands. Our findings provide new insights into how electrostatics can be employed to tune the catalytic activity of metalloenzymes and can thus contribute to the future design of new and highly efficient hydrogen‐abstraction catalysts.     

Methyl 4‐O‐β‐l‐fucopyranosyl α‐­d‐­glucopyranoside hemihydrate

The crystal structure of methyl 4‐O‐β‐l ‐fuco­pyran­osyl α‐d ‐gluco­pyran­oside hemihydrate C₁₃H₂₄O₁₀·0.5H₂O is organized in sheets with antiparallel strands, where hydro­phobic interaction accounts for partial stabilization. Infinite hydrogen‐bonding networks are observed within each layer as well as between layers; some of these hydrogen bonds are mediated by water mol­ecules. The conformation of the disaccharide is described by the glycosidic torsion angles: ?_H = ?6.1° and ψ_H = 34.3°. The global energy minimum conformation as calculated by molecular mechanics in vacuo has ?_H = ?58° and ψ_H = ?20°. Thus, quite substantial changes are observed between the in vacuo structure and the crystal structure with its infinite hydrogen‐bonding networks.     

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.     

Methyl 4‐O‐β‐d‐galactopyranosyl α‐d‐mannopyranoside methanol 0.375‐solvate

Methyl β‐d ‐galactopyranosyl‐(1→4)‐α‐d ‐mannopyranoside methanol 0.375‐solvate, C₁₃H₂₄O₁₁·0.375CH₃OH, (I), was crystallized from a methanol–ethanol solvent system in a glycosidic linkage conformation, with ϕ′ (O5_Gal—C1_Gal—O1_Gal—C4_Man) = −68.2 (3)° and ψ′ (C1_Gal—O1_Gal—C4_Man—C5_Man) = −123.9 (2)°, where the ring is defined by atoms O5/C1–C5 (monosaccharide numbering); C1 denotes the anomeric C atom and C6 the exocyclic hydroxymethyl C atom in the βGalp and αManp residues, respectively. The linkage conformation in (I) differs from that in crystalline methyl α‐lactoside [methyl β‐d ‐galactopyranosyl‐(1→4)‐α‐d ‐glucopyranoside], (II) [Pan, Noll & Serianni (2005). Acta Cryst. C 61 , o674–o677], where ϕ′ is −93.6° and ψ′ is −144.8°. An intermolecular hydrogen bond exists between O3_Man and O5_Gal in (I), similar to that between O3_Glc and O5_Gal in (II). The structures of (I) and (II) are also compared with those of their constituent residues, viz. methyl α‐d ‐mannopyranoside, methyl α‐d ‐glucopyranoside and methyl β‐d ‐galactopyranoside, revealing significant differences in the Cremer–Pople puckering parameters, exocyclic hydroxymethyl group conformations and intermolecular hydrogen‐bonding patterns.     

Poly[[diaqua‐μ‐4,4′‐bipyridine‐dinitratodi‐μ‐l‐tyrosinato‐dicopper(II)]: a chiral two‐dimensional coordination polymer

The title compound, [Cu₂(C₉H₁₀NO₃)₂(NO₃)₂(C₁₀H₈N₂)(H₂O)₂]_n, contains Cu^II atoms and l ‐tyrosinate (l ‐tyr) and 4,4′‐bipyridine (4,4′‐bipy) ligands in a 2:2:1 ratio. Each Cu atom is coordinated by one amino N atom and two carboxylate O atoms from two l ‐tyr ligands, one N atom from a 4,4′‐bipy ligand, a monodentate nitrate ion and a water molecule in an elongated octahedral geometry. Adjacent Cu atoms are bridged by the bidentate carboxylate groups into a chain. These chains are further linked by the bridging 4,4′‐bipy ligands, forming an undulated chiral two‐dimensional sheet. O—H...O and N—H...O hydrogen bonds connect the sheets in the [100] direction. This study offers useful information for the engineering of chiral coordination polymers with amino acids and 4,4′‐bipy ligands by considering the ratios of the metal ion and organic components.     

C3′‐Deoxygenation of Paromamine Catalyzed by a Radical S‐Adenosylmethionine Enzyme: Characterization of the Enzyme AprD4 and Its Reductase Partner AprD3

C3′‐deoxygenation of aminoglycosides results in their decreased susceptibility to phosphorylation thereby increasing their efficacy as antibiotics. However, the biosynthetic mechanism of C3′‐deoxygenation is unknown. To address this issue, aprD4 and aprD3 genes from the apramycin gene cluster in Streptomyces tenebrarius were expressed in E. coli and the resulting gene products were characterized in vitro. AprD4 is shown to be a radical S‐adenosylmethionine (SAM) enzyme, catalyzing homolysis of SAM to 5′‐deoxyadenosine (5′‐dAdo) in the presence of paromamine. [4′‐²H]‐Paromamine was prepared and used to show that its C4′‐H is transferred to 5′‐dAdo by AprD4, during which the substrate is dehydrated to a product consistent with 4′‐oxolividamine. In contrast, paromamine is reduced to a deoxy product when incubated with AprD4/AprD3/NADPH. These results show that AprD4 is the first radical SAM diol‐dehydratase and, along with AprD3, is responsible for 3′‐deoxygenation in aminoglycoside biosynthesis.