Renewable Resources Robert-Jan van Putten,†,‡ Jan C. van der Waal,† Ed de Jong,*,† Carolus B. Rasrendra,‡,⊥ Hero J. Heeres,*,‡ and Johannes G. de Vries* †Avantium Chemicals, Zekeringstraat 29, 1014 BV Amsterdam, the Netherlands ‡Department of Chemical Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands DSM Innovative Synthesis BV, P.O. Box 18, 6160 MD Geleen, the Netherlands Department of Chemical Engineering, Institut Teknologi Bandung, Ganesha 10, Bandung 40132, Indonesia

Hydroxymethylfurfural, A Versatile Platform Chemical Made from Renewable Resources

It was once widely held that nearly all reactions in biology were catalyzed via mechanisms involving paired electron species. Beginning approximately 40 years ago, this paradigm was repeatedly challenged as examples of enzymatic reactions involving organic radical intermediates began to emerge, and it is now well accepted that biochemical reactions often involve organic radicals. Indeed, some of the most intensely studied metalloenzymes, including cytochrome P450, methane monooxygenase, ribonucleotide reductase, and the adenosylcobalamin (B12) enzymes, catalyze reactions employing organic radical intermediates. As a general rule, enzymes utilizing radical mechanisms catalyze reactions that would be difficult or impossible to catalyze by polar mechanisms, most often involving H-atom abstraction from an unactivated C–H bond.

Among the more recent additions to the enzymes that catalyze radical reactions are the radical S-adenosylmethionine (radical SAM) enzymes, which were first classified as a superfamily in 2001.1 These enzymes utilize a [4Fe–4S] cluster and SAM to initiate a diverse set of radical reactions, in most or all cases via generation of a 5′-deoxyadenosyl radical (dAdo•) intermediate. Although 2001 marked the identification of this superfamily largely through bioinformatics, the discovery of iron metalloenzymes utilizing SAM to initiate radical reactions precedes this date by more than a decade. For example, early studies on the activation of pyruvate formate-lyase showed that it involved the generation of a stable protein radical,2 and was stimulated by the presence of iron, SAM, and an “activating component” from the cell extract now known to be the pyruvate-formate lyase activating enzyme (PFL-AE).3 The radical on PFL was ultimately shown to be located on a specific glycine residue,4 and was one of the first stable protein radicals characterized. PFL-AE was ultimately shown to contain a catalytically essential iron–sulfur cluster,5 and to use SAM as an essential component of PFL activation.6 The anaerobic ribonucleotide reductase, similar to PFL, contains a stable glycyl radical that was shown in early work to require an iron–sulfur cluster and SAM for activation.7 Likewise, preliminary investigations on lysine 2,3-aminomutase (LAM) published in 1970 demonstrated activation by ferrous ion and a strict requirement for SAM.8 Like PFL-AE, LAM was ultimately found to contain a catalytically essential iron–sulfur cluster.9 Work in Perry Frey’s lab showed that LAM used the adenosyl moiety of SAM to mediate hydrogen transfer in a manner similar to adenosylcobalamin-dependent rearrangements, implicating radical intermediates.10 Biotin synthase was first reported to require iron and SAM in 1995,11 and was subsequently shown to contain iron–sulfur clusters and to catalyze a radical reaction.12

These four enzyme systems (PFL/PFL-AE, aRNR, LAM, and biotin synthase) provided early indications of a new type of biological cofactor consisting of an iron–sulfur cluster and SAM, which initiate radical reactions using a fundamental new mechanism of catalysis.13 What none of us in the field in the early days probably anticipated, however, was just how ubiquitous these enzymes would turn out to be. The initial report of the superfamily by Sofia et al. identified ∼600 members;1 however, now that number is ∼48 100 members.14 These enzymes are found across the phylogenetic kingdom and catalyze an amazingly diverse set of reactions, the vast majority of which have yet to be characterized.

This Review will begin by summarizing unifying features of radical SAM enzymes, and in subsequent sections delve further into the biochemical, spectroscopic, structural, and mechanistic details for those enzymes that have been characterized. In most cases, these enzymes are grouped by reaction type; however, in two cases (syntheses of modified tetrapyrroles and complex metal cluster cofactors), we have chosen to group together several radical SAM enzymes that catalyze different reaction types but which act together in the same or related metabolic pathways.

Radical S-Adenosylmethionine Enzymes

Many biologically active small-molecule natural products produced by microorganisms derive their activities from sugar substituents. Changing the structures of these sugars can have a profound impact on the biological properties of the parent compounds. This realization has inspired attempts to derivatize the sugar moieties of these natural products through exploitation of the sugar biosynthetic machinery. This approach requires an understanding of the biosynthetic pathway of each target sugar and detailed mechanistic knowledge of the key enzymes. Scientists have begun to unravel the biosynthetic logic behind the assembly of many glycosylated natural products and have found that a core set of enzyme activities is mixed and matched to synthesize the diverse sugar structures observed in nature. Remarkably, many of these sugar biosynthetic enzymes and glycosyltransferases also exhibit relaxed substrate specificity. The promiscuity of these enzymes has prompted efforts to modify the sugar structures and alter the glycosylation patterns of natural products through metabolic pathway engineering and enzymatic glycodiversification. In applied biomedical research, these studies will enable the development of new glycosylation tools and generate novel glycoforms of secondary metabolites with useful biological activity.

Natural-Product Sugar Biosynthesis and Enzymatic Glycodiversification

Current interest in reacting carbonyl-containing molecules in aqueous media is primarily due to the growing emphasis on conversion of biomass to fuels and chemicals. Recently, solid Lewis acids have been shown to perform catalytic reactions with carbonyl-containing molecules such as sugars in aqueous media. Here, catalysis mediated by Lewis acids is briefly discussed, Lewis acid solids that perform catalysis in aqueous media are then described, and the review is concluded with a few comments on the outlook for the future.

http://www.chtf.stuba.sk/~szolcsanyi/education/files/Chemia%20heterocyklickych%20zlucenin/Prednaska%207/Doplnkove%20studijne%20materialy/Hydroxymethylfurfural/Activation%20of%20Carbonyl-Containing%20Molecules%20with%20Solid%20Lewis%20Acids%20in%20Aqueous%20Media.pdf

Activation of Carbonyl-Containing Molecules with Solid Lewis Acids in Aqueous Media

The enzymes involved in the biosynthesis of carbohydrates and the attachment of sugar units to biological acceptor molecules catalyse an array of chemical transformations and coupling reactions. In prokaryotes, both common sugar precursors and their enzymatically modified derivatives often become substituents of biologically active natural products through the action of glycosyltransferases. Recently, researchers have begun to harness the power of these biological catalysts to alter the sugar structures and glycosylation patterns of natural products both in vivo and in vitro. Biochemical and structural studies of sugar biosynthetic enzymes and glycosyltransferases, coupled with advances in bioengineering methodology, have ushered in a new era of drug development.

Unusual sugar biosynthesis and natural product glycodiversification

ion at 2-OH of the substrate, a process that also leads to further movement of this metal.310,315 It is proposed that the protein ligands Asp254 and Asp256 dissociate from Mg-2 at this stage and are replaced by a water molecule, O-1, and O-2 of the substrate (105).284,305 Thus, the developing negative charge at O-2 is stabilized by both Mg-1 and Mg-2, which in turn pulls the metal centers closer to establish a proper geometry to facilitate the isomerization step (105).305,308 As depicted in Scheme 33, after tautomerization the partial negative charge generated at O-1 may be stabilized by Lys182 (106).298,301,305,316 This lysine residue together with the metal ions confines the extended reaction intermediate in a syn-conformation and thus determines the stereochemical course of the hydride shift process.284,285 The Mg-2-bound water molecule has been proposed to be the proton donor to O-1 (106).277,285,310,317 Lys182 may be an alternative candidate for the active-site acid according to a Scheme 32 Scheme 33 4648 Chemical Reviews, 2000, Vol. 100, No. 12 He et al.

and Gautam Agnihotri

Papers

Novel enzymatic mechanisms in carbohydrate metabolism.