Features and applications of microbial sugar epimerases

Epimerization effects on coordination behaviours of phenanthroline-based phosphine-oxide ligands with uranyl ions

Epimers of the (1,10-phenanthroline-2,9-diyl)bis(ethyl(phenyl)phosphine oxide) (Et-Ph-BPPhen) ligand with two chiral centers (R,R/S,S and R,S) were synthesized. The configurational effects on the coordination ability and mechanism between these epimeric ligands and uranyl ions were thoroughly investigated. This work is helpful to reveal the effects of different conformations of epimeric ligands on their coordination properties.

Cloning and characterization of a new ribitol dehydrogenase from Providencia alcalifaciens RIMD 1656011

BACKGROUND

A new ribitol dehydrogenase gene was cloned from Providencia alcalifaciens RIMD 1656011 and expressed in Escherichia coli BL21. This study aimed to purify and characterize the ribitol dehydrogenase from P. alcalifaciens RIMD 1656011 and investigate its substrate specificity for potential use as an industrial enzyme.

RESULTS

The protein was purified by nickel affinity chromatography. The molecular mass of the purified enzyme was determined as ∼25 000 and 26 650 Da through sodium dodecyl sulfate polyacrylamide gel electrophoresis and liquid chromatography/mass spectrometry respectively. The result for native molecular mass (104 kDa) suggested that the enzyme functions as a tetramer. Optimum activity of the enzyme was determined at pH 10.0 and a temperature of 35 °C. Regarding its thermal stability, the enzyme retained 72, 72, 48 and 0% of its initial activity after 4 h at 25, 30, 40 and 50 °C respectively. The Km , kcat and kcat /Km values of the enzyme for the substrate ribitol were determined as 13.9 mmol L(-1) , 10.0 s(-1) and 0.71 L mmol(-1) s(-1) respectively. The Km of NAD(+) was 0.042 mmol L(-1) .

CONCLUSION

The substrate specificity indicated that the ribitol dehydrogenase from P. alcalifaciens RIMD 1656011 can be used for direct production of allitol from d-fructose without any by-product formation. © 2015 Society of Chemical Industry.

Structural and functional characterization of the Clostridium perfringens N-acetylmannosamine-6-phosphate 2-epimerase essential for the sialic acid salvage pathway

Pathogenic bacteria are endowed with an arsenal of specialized enzymes to convert nutrient compounds from their cell hosts. The essential N-acetylmannosamine-6-phosphate 2-epimerase (NanE) belongs to a convergent glycolytic pathway for utilization of the three amino sugars, GlcNAc, ManNAc, and sialic acid. The crystal structure of ligand-free NanE from Clostridium perfringens reveals a modified triose-phosphate isomerase (β/α)8 barrel in which a stable dimer is formed by exchanging the C-terminal helix. By retaining catalytic activity in the crystalline state, the structure of the enzyme bound to the GlcNAc-6P product identifies the topology of the active site pocket and points to invariant residues Lys(66) as a putative single catalyst, supported by the structure of the catalytically inactive K66A mutant in complex with substrate ManNAc-6P. (1)H NMR-based time course assays of native NanE and mutated variants demonstrate the essential role of Lys(66) for the epimerization reaction with participation of neighboring Arg(43), Asp(126), and Glu(180) residues. These findings unveil a one-base catalytic mechanism of C2 deprotonation/reprotonation via an enolate intermediate and provide the structural basis for the development of new antimicrobial agents against this family of bacterial 2-epimerases.

Complete 6-deoxy-D-altro-heptose biosynthesis pathway from Campylobacter jejuni: more complex than anticipated

The Campylobacter jejuni capsule is important for colonization and virulence in various infection models. In most strains, the capsule includes a modified heptose whose biological role and biosynthetic pathway are unknown. To decipher the biosynthesis pathway for the 6-deoxy-D-altro-heptose of strain 81-176, we previously showed that the 4,6-dehydratase WcbK and the reductase WcaG generated GDP-6-deoxy-D-manno-heptose, but the C3 epimerase necessary to form GDP-6-deoxy-D-altro-heptose was not identified. Herein, we characterized the putative C3/C5 epimerase Cjj1430 and C3/C5 epimerase/C4 reductase Cjj1427 from the capsular cluster. We demonstrate that GDP-6-deoxy-D-altro-heptose biosynthesis is more complex than anticipated and requires the sequential action of WcbK, Cjj1430, and Cjj1427. We show that Cjj1430 serves as C3 epimerase devoid of C5 epimerization activity and that Cjj1427 has no epimerization activity and only serves as a reductase to produce GDP-6-deoxy-D-altro-heptose. Cjj1430 and Cjj1427 are the only members of the C3/C5 epimerases and C3/C5 epimerase/C4 reductase families shown to have activity on a heptose substrate and to exhibit only one of their two to three potential activities, respectively. Furthermore, we show that although the reductase WcaG is not part of the main pathway, its presence and its product affect the outcome of the pathway in a complex regulatory loop involving Cjj1427. This work provides the grounds for the elucidation of similar pathways found in other C. jejuni strains and other pathogens. It provides new molecular tools for the synthesis of carbohydrate antigens useful for vaccination and for the screening of enzymatic inhibitors that may have antibacterial effects.

Purification and properties of phenolic acid decarboxylase from Candida guilliermondii

A heat-labile phenolic acid decarboxylase from Candida guilliermondii (an anamorph of Pichia guilliermondii) was purified to homogeneity by simple successive column chromatography within 3 days. The molecular mass was 20 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 36 kDa by gel-filtration chromatography, suggesting that the purified enzyme is a homodimer. The optimal pH and temperature were approximately 6.0 and 25°C. Characteristically, more than 50% of the optimal activity was observed at 0°C, suggesting that this enzyme is cold-adapted. The enzyme converted p-coumaric acid, ferulic acid, and caffeic acid to corresponding products with high specific activities of approximately 600, 530, and 46 U/mg, respectively. The activity was stimulated by Mg(2+) ions, whereas it was completely inhibited by Fe(2+), Ni(2+), Cu(2+), Hg(2+), 4-chloromericuribenzoate, N-bromosuccinimide, and diethyl pyrocarbonate. The enzyme was inducible and expressed inside the cells moderately by ferulic acid and p-coumaric acid and significantly by non-metabolizable 6-hydroxy-2-naphthoic acid.