Laurent Salmon

Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment

The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for d-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on d-glucose. These genes were heterologously overexpressed in Escherichia coli, and the recombinant proteins were purified and biochemically studied. This showed that d-arabinose is oxidized to 2-oxoglutarate by the consecutive action of a number of previously uncharacterized enzymes, including a d-arabinose dehydrogenase, a d-arabinonate dehydratase, a novel 2-keto-3-deoxy-d-arabinonate dehydratase, and a 2,5-dioxopentanoate dehydrogenase. Promoter analysis of these genes revealed a palindromic sequence upstream of the TATA box, which is likely to be involved in their concerted transcriptional control. Integration of the obtained biochemical data with genomic context analysis strongly suggests the occurrence of pentose oxidation pathways in both Archaea and Bacteria, and predicts the involvement of additional enzyme components. Moreover, it revealed striking genetic similarities between the catabolic pathways for pentoses, hexaric acids, and hydroxyproline degradation, which support the theory of metabolic pathway genesis by enzyme recruitment.

The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-d-arabinonohydroxamic acid

Phosphoglucose isomerase (EC 5.3.1.9) catalyzes the second step in glycolysis, the reversible isomerization of d-glucose 6-phosphate to d-fructose 6-phosphate. The reaction mechanism involves acid-base catalysis with proton transfer and proceeds through a cis-enediol(ate) intermediate. 5-Phospho-d-arabinonohydroxamic acid (5PAH) is a synthetic small molecule that resembles the reaction intermediate, differing only in that it has a nitrogen atom in place of C1. Hence, 5PAH is the best inhibitor of the isomerization reaction reported to date with a Ki of 2 × 10−7 M. Here we report the crystal structure of rabbit phosphoglucose isomerase complexed with 5PAH at 1.9 Å resolution. The interaction of 5PAH with amino acid residues in the enzyme active site supports a model of the catalytic mechanism in which Glu-357 transfers a proton between C1 and C2 and Arg-272 helps stabilize the intermediate. It also suggests a mechanism for proton transfer between O1 and O2.

Binding of 5‐phospho‐D‐arabinonohydroxamate and 5‐phospho‐D‐arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics

Type I phosphomannose isomerase (PMI) is a Zn‐dependent metalloenzyme involved in the isomerization of D‐fructose 6‐phosphate to D‐mannose 6‐phosphate. One of our laboratories has recently designed and synthesized 5‐phospho‐D‐arabinonohydroxamate (5PAH), an inhibitor endowed with a nanomolar affinity for PMI (Roux et al., Biochemistry 2004, 43, 2926). By contrast, the 5‐phospho‐D‐arabinonate (5PAA), in which the hydroxamate moiety is replaced by a carboxylate one, is devoid of inhibitory potency. Subsequent biochemical studies showed that in its PMI complex, 5PAH binds Zn(II) through its hydroxamate moiety rather than through its phosphate. These results have stimulated the present theoretical investigation in which we resort to the SIBFA polarizable molecular mechanics procedure to unravel the structural and energetical aspects of 5PAH and 5PAA binding to a 164‐residue model of PMI. Consistent with the experimental results, our theoretical studies indicate that the complexation of PMI by 5PAH is much more favorable than by 5PAA, and that in the 5PAH complex, Zn(II) ligation by hydroxamate is much more favorable than by phosphate. Validations by parallel quantum‐chemical computations on model of the recognition site extracted from the PMI‐inhibitor complexes, and totaling up to 140 atoms, showed the values of the SIBFA intermolecular interaction energies in such models to be able to reproduce the quantum‐chemistry ones with relative errors < 3%. On the basis of the PMI–5PAH SIBFA energy‐minimized structure, we report the first hypothesis of a detailed view of the active site of the zinc PMI complexed to the high‐energy intermediate analogue inhibitor, which allows us to identify active site residues likely involved in the proton transfer between the two adjacent carbons of the substrates.

Ribose 5-phosphate isomerase type B from Trypanosoma cruzi: kinetic properties and site-directed mutagenesis reveal information about the reaction mechanism

Trypanosoma cruzi, the human parasite that causes Chagas disease, contains a functional pentose phosphate pathway, probably essential for protection against oxidative stress and also for R5P (ribose 5-phosphate) production for nucleotide synthesis. The haploid genome of the CL Brener clone of the parasite contains one gene coding for a Type B Rpi (ribose 5-phosphate isomerase), but genes encoding Type A Rpis, most frequent in eukaryotes, seem to be absent. The RpiB enzyme was expressed in Escherichia coli as a poly-His tagged active dimeric protein, which catalyses the reversible isomerization of R5P to Ru5P (ribulose 5-phosphate) with Km values of 4 mM (R5P) and 1.4 mM (Ru5P). 4-phospho-D-erythronohydroxamic acid, an analogue to the reaction intermediate when the Rpi acts via a mechanism involving the formation of a 1,2-cis-enediol, inhibited the enzyme competitively, with an IC50 value of 0.7 mM and a Ki of 1.2 mM. Site-directed mutagenesis allowed the demonstration of a role for His102, but not for His138, in the opening of the ribose furanosic ring. A major role in catalysis was confirmed for Cys69, since the C69A mutant was inactive in both forward and reverse directions of the reaction. The present paper contributes to the know-ledge of the mechanism of the Rpi reaction; in addition, the absence of RpiBs in the genomes of higher animals makes this enzyme a possible target for chemotherapy of Chagas disease.

Synthesis and evaluation of a new inhibitor of phosphoglucose isomerases: the enediolate analogue 5-phospho-D-arabinohydroxamate

Designed as a high energy intermediate analogue inhibitor of the potent chemotherapeutic target phosphoglucose isomerases, 5-phospho-D-arabinohydroxamate was efficiently synthesized in a two steps procedure. To date, it proved to be the strongest competitive inhibitor with respect to substrate D-fructose-6-phosphate (Ki down to 98 nM and Km/Ki values up to 513). A comparative inhibition study of this compound and other known strong inhibitors on phosphoglucose isomerases from three different sources is also reported.

Synthesis and preliminary DNA-interaction studies of a new cationic porphyrin

Abstract A new water-soluble porphyrin containing benzyl-trimethylammonium groups was synthesized in a two-step sequence from tetraphenylporphyrin and preliminary studies show that it binds strongly to DNA in an outside manner and gives fairly stable complexes with nucleotides and nucleosides.

Polarizable water networks in ligand-metalloprotein recognition. Impact on the relative complexation energies of Zn-dependent phosphomannose isomerase with D-mannose 6-phosphate surrogates.

Using polarizable molecular mechanics, a recent study [de Courcy et al. J. Am. Chem. Soc., 2010, 132, 3312] has compared the relative energy balances of five competing inhibitors of the FAK kinase. It showed that the inclusion of structural water molecules was indispensable for an ordering consistent with the experimental one. This approach is now extended to compare the binding affinities of four active site ligands to the Type I Zn-metalloenzyme phosphomannose isomerase (PMI) from Candida albicans. The first three ones are the PMI substrate β-D-mannopyranose 6-phosphate (β-M6P) and two isomers, α-D-mannopyranose 6-phosphate (α-M6P) and β-D-glucopyranose 6-phosphate (β-G6P). They have a dianionic 6-phosphate substituent and differ by the relative configuration of the two carbon atoms C1 and C2 of the pyranose ring. The fourth ligand, namely 6-deoxy-6-dicarboxymethyl-β-D-mannopyranose (β-6DCM), is a substrate analogue that has the β-M6P phosphate replaced by the nonhydrolyzable phosphate surrogate malonate. In the energy-minimized structures of all four complexes, one of the ligand hydroxyl groups binds Zn(II) through a water molecule, and the dianionic moiety binds simultaneously to Arg304 and Lys310 at the entrance of the cavity. Comparative energy-balances were performed in which solvation of the complexes and desolvation of PMI and of the ligands are computed using the Langlet-Claverie continuum reaction field procedure. They resulted into a more favorable balance in favor of β-M6P than α-M6P and β-G6P, consistent with the experimental results that show β-M6P to act as a PMI substrate, while α-M6P and β-G6P are inactive or at best weak inhibitors. However, these energy balances indicated the malonate ligand β-6DCM to have a much lesser favorable relative complexation energy than the substrate β-M6P, while it has an experimental 10-fold higher affinity than it on Type I PMI from Saccharomyces cerevisiae. The energy calculations were validated by comparison with parallel ab initio quantum chemistry on model binding sites extracted from the energy-minimized PMI-inhibitor complexes. We sought to improve the models upon including explicit water molecules solvating the dianionic moieties in their ionic bonds with the Arg304 and Lys310 side-chains. Energy-minimization resulted in the formation of three networks of structured waters. The first water of each network binds to one of the three accessible anionic oxygens. The networks extend to PMI residues (Asp17, Glu48, Asp300) remote from the ligand binding site. The final comparative energy balances also took into account ligand desolvation in a box of 64 waters. They now resulted into a large preference in favor of β-6DCM over β-M6P. The means to further augment the present model upon including entropy effects and sampling were discussed. Nevertheless a clear-cut conclusion emerging from this as well as our previous study on FAK kinase is that both polarization and charge-transfer contributions are critical elements of the energy balances.

Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily.

The archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.

Poly(pyrrole manganese porphyrin) film electrode as a catalyst in electro-assisted oxidation reactions using molecular oxygen: comparison with described homogeneous systems

Abstract Oxidation reactions of cis -cyclooctene and 2,6-di-t-butylphenol (DTBP) with molecular oxygen, under atmospheric pressure, in acetonitrile and dichloromethane solutions are described using a manganese porphyrin-coated electrode as the catalyst. The results obtained are compared with those of other manganese porphyrin catalytic systems employed in the homogeneous phase. One remarkable aspect of these results is the large activity of the porphyrin catalyst when it is attached on to the electrode. In addition, these results confirm the stability of such polymer films.

Competitive inhibitors of yeast phosphoglucose isomerase: synthesis and evaluation of new types of phosphorylated sugars from the synthon d-arabinonolactone-5-phosphate

Designed as competitive inhibitors of the isomerization reaction catalyzed by the potential chemotherapeutic target phosphoglucose isomerases (PGI), D-arabinonamide-5-phosphate and D-arabinohydrazine-5-phosphate were synthesized and fully characterized. These new types of phosphorylated sugar derivatives were easily and efficiently obtained in a one-step procedure from the promising synthon D-arabinono-1,4-lactone 5-phosphate. These two compounds proved to be new good competitive inhibitors of yeast PGI with the substrate D-fructose-6-phosphate, though not as strong as D-arabinohydroxamic acid-5-phosphate. Overall, our results are in accord with the postulated 1,2-cis-enediolate species as a probable high-energy intermediate of the PGI-catalyzed reaction.