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1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum

Warlick BP, Evans BS, Erb TJ, Ramagopal UA, Sriram J, Imker HJ, Sauder JM, Bonanno JB, Burley SK, Tabita FR, Almo SC, Sweedler JS, Gerlt JA (2012) Biochemistry 51, 8324-6. PMCID: PMC3490199

This paper follows up on the work of Erb et al. and describes a biosynthetic pathway for the generation of 1‑deoxy‑D‑xylulose 5‑phosphate in Rhodospirillum rubrum via a novel methylsulfurylase.   This work demonstrates the how initial elucidation of a given function often seques into discovery of linked pathways and thereby facilitates a more holistic understanding of the metabolic universe.  

ABSTRACT

Rhodospirillum rubrum produces 5-methylthioadenosine (MTA) from S-adenosylmethionine in polyamine biosynthesis; however, R. rubrum lacks the classical methionine salvage pathway. Instead, MTA is converted to 5-methylthio-d-ribose 1-phosphate (MTR 1-P) and adenine; MTR 1-P is isomerized to 1-methylthio-d-xylulose 5-phosphate (MTXu 5-P) and reductively dethiomethylated to 1-deoxy-d-xylulose 5-phosphate (DXP), an intermediate in the nonmevalonate isoprenoid pathway [Erb, T. J., et al. (2012) Nat. Chem. Biol., in press]. Dethiomethylation, a novel route to DXP, is catalyzed by MTXu 5-P methylsulfurylase. An active site Cys displaces the enolate of DXP from MTXu 5-P, generating a methyl disulfide intermediate.

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Abstract Image

Figure 1. Reactions catalyzed by RLPs (A) in the classical methionine salvage pathway in Bacilli and (B) in the production of DXP in R. rubrum.

Figure 2. Active site of the cupin from R. rubrum (Protein Data Bank entry 3JZV).

Figure 3. 1H NMR spectra of the cupin substrates and products. (A) Mixture of MTRu 1-P and MTXu 1-P in H2O. (B) After reaction with cupin in H2O in the presence of excess DTT (spectrum obtained with solvent suppression). (C) Authentic DXP in H2O. (D) Mixture of MTRu 1-P and MTXu 1-P in D2O. (E) After reaction with cupin in D2O. The resonances are color-coded according to the structures in Figure 1.

Figure 4. Possible mechanisms for the cupin-catalyzed reaction. (A) Proton abstraction followed by elimination and reduction. (B) Displacement of the enolate anion of DXP followed by reduction.

Figure 5. Localization of the methanethiol adduct to Cys 121. (A) Doubly charged tryptic peptide corresponding to residues 112–128 with a methanethiol disulfide modification. (B) Tandem mass spectrum of the peptide ion in panel A. The complementary fragment ion pair b10+ and y12+ localize the methanethiol modification to Cys 121.

Scheme 1

Reprinted with permission from the Journal of Biological Chemistry. © 2012 by the American Chemical Society