Structure of <scp>l</scp>‐rhamnose isomerase in complex with <scp>l</scp>‐rhamnopyranose demonstrates the sugar‐ring opening mechanism and the role of a substrate sub‐binding site

Yoshida, Hiromi; Yoshihara, Akihide; Teraoka, Misa; Yamashita, Satoshi; Izumori, Ken; Kamitori, Shigehiro

doi:10.1016/j.fob.2012.11.008

Cited by 12 publications

(8 citation statements)

References 34 publications

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“…In addition, ring opening is a common process for the first step of sugar isomerization/epimerization, as exemplified by phosphoglucose isomer-ase, galactose mutarotase, and rhamnose isomerase (13,25,26) as well as aAGE and SeYihS (11,12). The proposed mechanisms indicated that acid (A-H) and base (B:…”

Section: Structural Insights Into the Ring Opening/closurementioning

confidence: 99%

Structural Insights into the Epimerization of β-1,4-Linked Oligosaccharides Catalyzed by Cellobiose 2-Epimerase, the Sole Enzyme Epimerizing Non-anomeric Hydroxyl Groups of Unmodified Sugars

Fujiwara

Saburi

Matsui

et al. 2014

Journal of Biological Chemistry

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Background:The details of the catalytic mechanism of cellobiose 2-epimerase (CE) remains unclear. Results: The crystal structures of Rhodothermus marinus CE in the apo form and complexes with its substrates/products 4-O-␤-D-glucopyranosyl-D-mannnose, epilactose, or cellobiitol (reaction intermediate analog) were elucidated. Conclusion: Epimerization catalyzed by CE proceeds through ring opening, deprotonation/reprotonation, carbon-carbon bond rotation, and ring closure. Significance: This study yielded structural insights into epimerization catalyzed by CE.

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Section: Structural Insights Into the Ring Opening/closurementioning

confidence: 99%

Structural Insights into the Epimerization of β-1,4-Linked Oligosaccharides Catalyzed by Cellobiose 2-Epimerase, the Sole Enzyme Epimerizing Non-anomeric Hydroxyl Groups of Unmodified Sugars

Fujiwara

Saburi

Matsui

et al. 2014

Journal of Biological Chemistry

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“…In addition, E. coli possesses L-rhamnose mutarotase (RhaM, EC 5.1.3.32), which facilitates the interconversion of the ␣ and ␤ anomers of L-rhamnopyranose, enhancing the rate of rhamnose catabolism (9); the catalytic mechanism of mutarotation can be envisaged by examining the crystal structures of the enzymes from E. coli and Rhizobium leguminosarum (9,10). By analogy of a proposed catalytic mechanism of Pseudomonas stutzeri L-rhamnose isomerase, E. coli RhaA might preferentially isomerize ␤-L-rhamnopyranose to ␤-Lrhamnulofuranose (11). This assumption is supported by the crystal structure of the complex of E. coli RhaB with ␤-L-rhamnulofuranose and ADP (12) (Fig.…”

mentioning

confidence: 99%

Regulation of the rhaEWRBMA Operon Involved in l -Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis

et al. 2016

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The Bacillus subtilis rhaEWRBMA (formerly yuxG-yulBCDE) operon consists of four genes encoding enzymes for L-rhamnose catabolism and the rhaR gene encoding a DeoR-type transcriptional regulator. DNase I footprinting analysis showed that the RhaR protein specifically binds to the regulatory region upstream of the rhaEW gene, in which two imperfect direct repeats are included. Gel retardation analysis revealed that the direct repeat farther upstream is essential for the high-affinity binding of RhaR and that the DNA binding of RhaR was effectively inhibited by L-rhamnulose-1-phosphate, an intermediate of L-rhamnose catabolism. Moreover, it was demonstrated that the CcpA/P-Ser-HPr complex, primarily governing the carbon catabolite control in B. subtilis, binds to the catabolite-responsive element, which overlaps the RhaR binding site. In vivo analysis of the rhaEW promoter-lacZ fusion in the background of ccpA deletion showed that the L-rhamnose-responsive induction of the rhaEW promoter was negated by the disruption of rhaA or rhaB but not rhaEW or rhaM, whereas rhaR disruption resulted in constitutive rhaEW promoter activity. These in vitro and in vivo results clearly indicate that RhaR represses the operon by binding to the operator site, which is detached by L-rhamnulose-1-phosphate formed from L-rhamnose through a sequence of isomerization by RhaA and phosphorylation by RhaB, leading to the derepression of the operon. In addition, the lacZ reporter analysis using the strains with or without the ccpA deletion under the background of rhaR disruption supported the involvement of CcpA in the carbon catabolite repression of the operon. IMPORTANCESince L-rhamnose is a component of various plant-derived compounds, it is a potential carbon source for plant-associating bacteria. Moreover, it is suggested that L-rhamnose catabolism plays a significant role in some bacteria-plant interactions, e.g., invasion of plant pathogens and nodulation of rhizobia. Despite the physiological importance of L-rhamnose catabolism for various bacterial species, the transcriptional regulation of the relevant genes has been poorly understood, except for the regulatory system of Escherichia coli. In this study, we show that, in Bacillus subtilis, one of the plant growth-promoting rhizobacteria, the rhaEWRBMA operon for L-rhamnose catabolism is controlled by RhaR and CcpA. This regulatory system can be another standard model for better understanding the regulatory mechanisms of L-rhamnose catabolism in other bacterial species. Bacillus subtilis is a soil-dwelling bacterium that has been extensively and closely studied as a Gram-positive model bacterium. B. subtilis species have often been isolated from the rhizosphere of various terrestrial plants; many of them have been shown to be plant growth-promoting rhizobacteria whose association with the plant roots enhances the adaptive potential of plants and increases their growth (1). Interestingly, B. subtilis is also a saprophytic bacterium that secretes various degrading enzymes, incl...

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“…Different studies suggest the prevalence of the cyclic form (pyranose, furanose) of the selected monosaccharides (hexoses, pentose, and their derivatives) in the aqueous solutions, which can be explained by the fact that the formed cyclic hemiacetals are strain-free and more stable than the open-chain structure [56][57][58][59]. Based on the previous research works on the determination of the characteristic anomeric forms of the selected monosaccharides [60][61][62][63][64][65][66][67] and the above-mentioned findings (Table 1), the following compounds are further considered as targeting foulants: β-D-glucopyranose (Glc), β-D-galactopyranose (Gal), β-D-mannopyranose (Man), α-D-glucopyranuronic acid (GlcUA), β-L-rhamnopyranose (Rha), β-L-fucopyranose (Fuc), α-L-arabinofuranose (Ara), and β-D-glucosamine (GlcN).…”

Section: The Structure and Active Centers Of The Studied Foulantsmentioning

confidence: 99%

Computational Thermodynamic Analysis of the Interaction between Coagulants and Monosaccharides as a Tool to Quantify the Fouling Potential Reduction in the Biofilm Membrane Bioreactor

Kulesha

Ratnaweera

2019

Water

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The membrane bioreactor (MBR) and the biofilm membrane bioreactor (BF-MBR) are among key solutions to water scarcity; however, membrane fouling is the major bottleneck for any expansion of these technologies. Prepolymerized aluminum coagulants tend to exhibit the greatest extent of fouling alleviation, with the reduction of soluble microbial products (SMPs) being among the governing mechanisms, which, nevertheless, has been poorly understood. This current study demonstrates that the investigation of the chemical coordination of monosaccharides, which are the major foulants in MBR and BF-MBR, to the main hydrolysis species of the prepolymerized aluminum coagulant, is among the key approaches to the comprehension of the fouling mitigation mechanisms in BF-MBR. Quantum chemical and thermodynamic calculations, together with the multivariate chemometric analysis, allowed the team to determine the principal mechanisms of the SMPs removal, understand the thermodynamic patterns of fouling mitigation, develop the model for the prediction of the fouling mitigation based on the thermodynamic stability of the inorganic-organic complexes, and classify these complexes into thermodynamically stable and less stable species. The results of the study are practically significant for the development of plant surveillance and automated process control with regard to MBR and BF-MBR systems.This gel layer is usually intertwined with the cake matrix, therefore it is highly complicated to distinguish either of them [9]. The formation of the cake layer, as well as the gel matrix at the membrane surface, are governed by the pressure-driven convective flow from the bulk mixed liquor solution to the membrane during filtration [7,9,10].Concentration polarization (CP) is the other type of solute fouling, which accompanies every filtration system, being, however, of marginal importance in the MBR/BF-MBR operation [9,11]. This phenomenon is entailed by the tendency of the solutes, rejected by the membrane, to accumulate at the membrane-solution interface within the concentration boundary region, driven by the concentration gradients, and to form a highly concentrated zone, called a concentration polarization layer. In contrast to the cake and gel layers, the transport within the concentration polarization region is diffusion, described by the Fick's first law [7,9,10]. The solids can diffuse back to the bulk mixed liquor in the CP layer, if they are not entrapped in the gel or cake layer. The concentration polarization model and the mechanisms and mathematical description of cake layer compaction are explained in detail by Yoon [12].Membrane pore blockage is mainly attributed to the accumulation of the solutes and colloids in the membrane pores and on the membrane surface, which comprises complete, internal, and intermediate pore blocking mechanisms. Membrane pore blockage, altogether with the cake filtration during the dead-end membrane filtration, was comprehensively described by Hermia's pore-blocking models, represented elsewhere [5,8,[13][1...

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Structure of l‐rhamnose isomerase in complex with l‐rhamnopyranose demonstrates the sugar‐ring opening mechanism and the role of a substrate sub‐binding site

Cited by 12 publications

References 34 publications

Structural Insights into the Epimerization of β-1,4-Linked Oligosaccharides Catalyzed by Cellobiose 2-Epimerase, the Sole Enzyme Epimerizing Non-anomeric Hydroxyl Groups of Unmodified Sugars

Structural Insights into the Epimerization of β-1,4-Linked Oligosaccharides Catalyzed by Cellobiose 2-Epimerase, the Sole Enzyme Epimerizing Non-anomeric Hydroxyl Groups of Unmodified Sugars

Regulation of the rhaEWRBMA Operon Involved in l -Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis

Computational Thermodynamic Analysis of the Interaction between Coagulants and Monosaccharides as a Tool to Quantify the Fouling Potential Reduction in the Biofilm Membrane Bioreactor

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