Studies on the Biosynthesis of Menaquinone (Vitamin K) and on the Catabolism of Pseudouridine

The present work describes studies aimed at characterizing enzymes involved in bacterial metabolic pathways using a variety of biochemical methods, analytical techniques and structural studies. The first study explains the structural and biochemical characterization of a C-glycosidase involved in pseudouridine catabolic pathway. Our studies suggested that its mechanism is significantly different from the previously reported glycosidases. The second study describes the discovery and mechanistic characterization of a radical SAM enzyme involved in a new menaquinone biosynthetic pathway. This enzyme represents a unique reaction motif in radical SAM enzymology. Pseudouridine (Ψ), the most abundant modification in RNA, is synthesized using Ψ synthase. Recently, a pathway for the degradation of Ψ was described in Escherichia coli. In this pathway, Ψ is first converted to Ψ 5′-monophosphate (ΨMP) by Ψ kinase and then ΨMP is degraded by ΨMP glycosidase to uracil and ribose 5- phosphate. The structural studies on the ΨMP glycosidase and its mutant (K166A) suggested that the reaction utilizes a Lys166-substrate adduct during catalysis. Biochemical studies on ΨMP glycosidase further confirmed the existence of a lysine adduct and allowed us to identify roles for specific active site residues. ΨMP glycosidase catalyzes the cleavage of the C−C glycosidic bond through a novel ribose ring-opening mechanism. This is the first mechanistically characterized C-glycosidase. Menaquinone (MK, vitamin K2) is a lipid soluble molecule that participates in the bacterial electron transport chain. In mammalian cells, MK functions as an essential vitamin for the activation of various proteins involved in blood clotting and bone metabolism. Recently, a new pathway for the biosynthesis of this cofactor was discovered in Streptomyces coelicolor A3(2) in which chorismate is converted to aminofutalosine in a reaction catalyzed by MqnA and an unidentified enzyme. Here, we reconstitute the biosynthesis of aminofutalosine and demonstrate that the missing enzyme (aminofutalosine synthase, MqnE) is a radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3-[(1-carboxyvinyl) oxy] benzoic acid. This is a new reaction type in the radical SAM superfamily. The substrate analogs based mechanistic investigation suggested that MqnE catalyzes a unique radical rearrangement reaction, unprecedented in biological chemistry

In vitro biosynthetic studies of bottromycin expand the enzymatic capabilities of the YcaO superfamily

The bottromycins belong to the ribosomally synthesized and posttranslationally modified peptide (RiPP) family of natural products. Bottromycins exhibit unique structural features, including a hallmark macrolactamidine ring and thiazole heterocycle for which divergent members of the YcaO superfamily have been biosynthetically implicated. Here we report the in vitro reconstitution of two YcaO proteins, BmbD and BmbE, responsible for the ATP-dependent cyclodehydration reactions that yield thiazoline- and macrolactamidine-functionalized products, respectively. We also establish the substrate tolerance for BmbD and BmbE and systematically dissect the role of the follower peptide, which we show serves a purpose similar to canonical leader peptides in directing the biosynthetic enzymes to the substrate. Lastly, we leverage the expanded capabilities of YcaO proteins to conduct an extensive bioinformatic survey to classify known YcaO chemistry. This analysis predicts new functions remain to be uncovered within the superfamily

Menaquinone Biosynthesis: Formation of Aminofutalosine Requires a Unique Radical SAM Enzyme

Menaquinone (MK, vitamin K₂) is a lipid-soluble molecule that participates in the bacterial electron transport chain. In mammalian cells, MK functions as an essential vitamin for the activation of various proteins involved in blood clotting and bone metabolism. Recently, a new pathway for the biosynthesis of this cofactor was discovered in <i>Streptomyces coelicolor</i> A3(2) in which chorismate is converted to aminofutalosine in a reaction catalyzed by MqnA and an unidentified enzyme. Here, we reconstitute the biosynthesis of aminofutalosine and demonstrate that the missing enzyme (aminofutalosine synthase, MqnE) is a radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3-[(1-carboxyvinyl)­oxy]­benzoic acid. This is a new reaction type in the radical SAM superfamily

Pseudouridine Monophosphate Glycosidase: A New Glycosidase Mechanism

Pseudouridine (Ψ), the most abundant modification in RNA, is synthesized in situ using Ψ synthase. Recently, a pathway for the degradation of Ψ was described [Preumont, A., Snoussi, K., Stroobant, V., Collet, J. F., and Van Schaftingen, E. (2008) <i>J. Biol. Chem. 283</i>, 25238–25246]. In this pathway, Ψ is first converted to Ψ 5′-monophosphate (ΨMP) by Ψ kinase and then ΨMP is degraded by ΨMP glycosidase to uracil and ribose 5-phosphate. ΨMP glycosidase is the first example of a mechanistically characterized enzyme that cleaves a C–C glycosidic bond. Here we report X-ray crystal structures of <i>Escherichia coli</i> ΨMP glycosidase and a complex of the K166A mutant with ΨMP. We also report the structures of a ring-opened ribose 5-phosphate adduct and a ring-opened ribose ΨMP adduct. These structures provide four snapshots along the reaction coordinate. The structural studies suggested that the reaction utilizes a Lys166 adduct during catalysis. Biochemical and mass spectrometry data further confirmed the existence of a lysine adduct. We used site-directed mutagenesis combined with kinetic analysis to identify roles for specific active site residues. Together, these data suggest that ΨMP glycosidase catalyzes the cleavage of the C–C glycosidic bond through a novel ribose ring-opening mechanism

Measurement of Kinetics and Active Site Distances in Metalloenzymes Using Paramagnetic NMR with ¹³C Hyperpolarization

Paramagnetic relaxation enhancement (PRE) conjoint with hyperpolarized NMR reveals structural information on the enzyme–product complex in an ongoing metalloenzyme-catalyzed reaction. Substrates of pseudouridine monophosphate glycosidase are hyperpolarized using the dynamic nuclear polarization (DNP) method. Time series of ¹³C NMR spectra are subsequently measured with the enzyme containing diamagnetic Mg²⁺ or paramagnetic Mn²⁺ ions in the active site. The differences of the signal evolution and line widths in the Mg²⁺ vs Mn²⁺ reactions are explained through PRE in the enzyme-bound product, which is in fast exchange with its free form. Here, a strong distance dependence of the paramagnetically enhanced relaxation rates enables the calculation of distances from product atoms to the metal center in the complexed structure. The same method can be used to add structural information to real-time characterizations of chemical processes involving compounds with naturally present or artificially introduced paramagnetic sites

Aminofutalosine Synthase: Evidence for Captodative and Aryl Radical Intermediates Using β‑Scission and S_RN1 Trapping Reactions

Aminofutalosine synthase (MqnE) is a radical SAM enzyme involved in the menaquinone biosynthetic pathway. In this communication, we propose a novel mechanism for this reaction involving the addition of the adenosyl radical to the substrate double bond to form a captodative radical followed by rearrangement and decarboxylation to form an aryl radical anion which is then oxidized by the [4Fe–4S]⁺² cluster. Consistent with this proposal, we describe the trapping of the captodative radical and the aryl radical anion using radical triggered C–Br fragmentation reactions. We also describe the trapping of the captodative radical by replacing the vinylic carboxylic acid with an amide

Mechanism of a Class C Radical <i>S</i>‑Adenosyl‑l‑methionine Thiazole Methyl Transferase

The past decade has seen the discovery of four different classes of radical <i>S</i>-adenosylmethionine (rSAM) methyltransferases that methylate unactivated carbon centers. Whereas the mechanism of class A is well understood, the molecular details of methylation by classes B–D are not. In this study, we present detailed mechanistic investigations of the class C rSAM methyltransferase TbtI involved in the biosynthesis of the potent thiopeptide antibiotic thiomuracin. TbtI <i>C</i>-methylates a Cys-derived thiazole during posttranslational maturation. Product analysis demonstrates that two SAM molecules are required for methylation and that one SAM (SAM1) is converted to 5′-deoxyadenosine and the second SAM (SAM2) is converted to <i>S</i>-adenosyl-l-homocysteine (SAH). Isotope labeling studies show that a hydrogen is transferred from the methyl group of SAM2 to the 5′-deoxyadenosine of SAM1 and the other two hydrogens of the methyl group of SAM2 appear in the methylated product. In addition, a hydrogen appears to be transferred from the β-position of the thiazole to the methyl group in the product. We also show that the methyl protons in the product can exchange with solvent. A mechanism consistent with these observations is presented that differs from other characterized radical SAM methyltransferases