Structural Insights into the Monosaccharide Specificity of Escherichia coli Rhamnose Mutarotase

Ryu, Kyoung‐Seok; Kim, Jung-In; Cho, Sungjae; Park, Dongkyu; Park, Chankyu; Cheong, Hae‐Kap; Lee, Jie‐Oh; Choi, Byong‐Seok

doi:10.1016/j.jmb.2005.03.047

Cited by 27 publications

(30 citation statements)

References 29 publications

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“…7). A triad interaction consisting of a hydrogen bond, cation-, and salt-bridge interaction between R41, Y77, and either D72 or D47 would be similar to other amino acid triad interactions that have been reported (52)(53)(54). However, the D72 residue alone appears to make no contribution to the stability of the KIR D1 domain (Fig.…”

Section: Discussionsupporting

confidence: 59%

A Single Polymorphism Disrupts the Killer Ig-Like Receptor 2DL2/2DL3 D1 Domain

VandenBussche

Dakshanamurthy

Posch

et al. 2006

The Journal of Immunology

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Genetic polymorphisms found in the killer Ig-like receptor (KIR), two domains, long cytoplasmic tail 2/3 (KIR2DL2/3) locus are responsible for the differential binding of KIR2DL2/3 allelic products with their HLA-C ligands and have been associated with the resolution of hepatitis C infection. In our study, a KIR CD3ζ fusion-binding assay did not detect any interaction between the KIR2DL2*004 extracellular domain and several putative KIR2DL2/3 ligands. To determine the amino acid polymorphism(s) responsible for the KIR2DL2*004 phenotype, we mutated the polymorphic residues of full-length KIR and expressed them in human Jurkat cells. Flow cytometry analysis failed to detect the surface expression of receptors containing a threonine at position 41 (T41), a polymorphism specific to KIR2DL2*004. Confocal microscopy showed that receptors containing T41 were retained inside the cell and had a perinuclear localization, possibly indicating that their extracellular domain was misfolded. Most KIR2DL2/3 alleles possess an arginine at position 41 (R41), and we predicted through molecular modeling and demonstrated by mutagenesis that R41 most likely interacts with the nearby residues Y77 and D47. Interaction between these residues would maintain C strand contact with the C′ and F strands of the D1 domain β-sheet. Furthermore, R41 and Y77 are conserved in the C and F strand amino acid alignments of Ig-like superfamily members, and may therefore be necessary for the structural integrity of other immune response proteins. Our data indicate that the extracellular T41 polymorphism encoded by the KIR2DL2*004 allele most likely results in misfolding of the D1 domain and complete intracellular retention of the receptor.

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Section: Discussionsupporting

confidence: 59%

A Single Polymorphism Disrupts the Killer Ig-Like Receptor 2DL2/2DL3 D1 Domain

VandenBussche

Dakshanamurthy

Posch

et al. 2006

The Journal of Immunology

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“…Mutarotases facilitate the interconversion of ␣ and ␤ anomers where the stereochemically less-favored anomer is required for a subsequent step in a catabolic sequence. Three such examples have so far been identified, including L-rhamnose mutarotase (YiiL in E. coli) (30,31), galactose mutarotase (GalM) (5,6,8,9,14,36,37,38,39), and fucose mutarotase (FucU) (16,30). In this report, we characterize rhaU from R. leguminosarum and provide evidence that is consistent with the hypothesis that RhaU is an L-rhamnose mutarotase.…”

supporting

confidence: 77%

RhaU of Rhizobium leguminosarum Is a Rhamnose Mutarotase

Richardson

Carpena²,

Switala

et al. 2008

J Bacteriol

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Of the nine genes comprising the L-rhamnose operon of Rhizobium leguminosarum, rhaU has not been assigned a function. The construction of a ⌬rhaU strain revealed a growth phenotype that was slower than that of the wild-type strain, although the ultimate cell yields were equivalent. The transport of L-rhamnose into the cell and the rate of its phosphorylation were unaffected by the mutation. RhaU exhibits weak sequence similarity to the formerly hypothetical protein YiiL of Escherichia coli that has recently been characterized as an L-rhamnose mutarotase. To characterize RhaU further, a His-tagged variant of the protein was prepared and subjected to mass spectrometry analysis, confirming the subunit size and demonstrating its dimeric structure. After crystallization, the structure was refined to a 1.6-Å resolution to reveal a dimer in the asymmetric unit with a very similar structure to that of YiiL. Soaking a RhaU crystal with L-rhamnose resulted in the appearance of ␤-L-rhamnose in the active site.Rhizobium leguminosarum bv. trifolii is a gram-negative soil bacterium that can form symbiotic associations with various species of clover. The plant provides the bacteria with energy for growth, and in return the bacteria provide the plant with fixed nitrogen from nitrogen-fixing nodules. Competition for nodule occupancy exists among strains of Rhizobium within the rhizosphere (10, 40), and strains of R. leguminosarum unable to catabolize L-rhamnose are compromised in their ability to compete for nodule occupancy (24).L-Rhamnose is a 6-deoxyhexose monosaccharide found in the mucilage of a number of legume plants and is a constituent of pectin in the form of rhamnogalacturonan within the cell walls of dicotyledonous plants (17,20). The 11-kb L-rhamnose locus in R. leguminosarum comprises L-rhamnose transport and catabolism genes (24, 28) organized in two divergently transcribed operons controlled by a negative regulator, rhaR (28). One transcript contains rhaD and rhaI, encoding a dehydrogenase/aldolase and an isomerase, respectively, while the other consists of rhaRSTPQUK (28). rhaS, rhaT, rhaP, and rhaQ encode the components of an ABC transporter, including a periplasmic sugar binding protein, an ABC ATPase, and two permeases, respectively (3). Within the L-rhamnose catabolic pathway, the enzymatic action of the kinase, encoded by rhaK, has been shown to precede the action of the dehydrogenase and the isomerase encoded by rhaD and rhaI, respectively (28). Moreover, the biochemical activity of the kinase appears to be necessary for L-rhamnose transport (29).Among the nine genes in the operon, only rhaU does not have an assigned role, and database searches revealed a number of similar open reading frames, none of which had an assigned function. However, YiiL, originally annotated as a hypothetical protein from the Escherichia coli genome, has recently been shown to be an L-rhamnose mutarotase, providing a strong clue to the identity of RhaU. Mutarotases facilitate the interconversion of ␣ and ␤ anomers where the stere...

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“…In E. coli, the genes for rhamnose catabolism constitute the rhaT gene, the rhaSR operon, and the rhaBAD (possibly rha-BADM) operon, which are contiguously arranged in this order; however, the direction of the rhaSR operon is opposite to those of the others so that the rhaS and rhaB promoters are close to each other (9,19). This gene organization is widely conserved in the family Enterobacteriaceae, including the genera Enterobacter, Klebsiella, Pantoea, Salmonella, Shigella, Yersinia, and Escherichia, albeit to slight differences in the constituent members in some species (7,43).…”

Section: Discussionmentioning

confidence: 99%

“…1). 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).…”

mentioning

confidence: 99%

“…It was reported that, in the E. coli genome, genes encoding the rhamnose transporter (RhaT), the rhamnose catabolic enzymes (RhaA, RhaB, and RhaD), and the rhamnose-responsive transcriptional activators (RhaS and RhaR) are assembled to form the rhaSR and rhaBAD operons and the rhaT gene, which are located adjacent to one another. Because the rhaM gene is situated just downstream of the rhaD gene in the same direction as the rhaBAD operon, the rhaM gene might be integrated into the operon members, although it has not been experimentally confirmed (9,19). Unlike B. subtilis RhaR, both RhaS and RhaR from E. coli belong to the AraC/XylS family and act as activators; however, they have different functions.…”

mentioning

confidence: 99%

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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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Structural Insights into the Monosaccharide Specificity of Escherichia coli Rhamnose Mutarotase

Cited by 27 publications

References 29 publications

A Single Polymorphism Disrupts the Killer Ig-Like Receptor 2DL2/2DL3 D1 Domain

A Single Polymorphism Disrupts the Killer Ig-Like Receptor 2DL2/2DL3 D1 Domain

RhaU of Rhizobium leguminosarum Is a Rhamnose Mutarotase

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

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