Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil

Nakamura, Akira

doi:10.1099/ijsem.0.000508

Cited by 21 publications

(7 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The third hit was scyllo-inositol dehydrogenase (sIDH) from Paracoccus laeviglucosivorans (PlsIDH), whose crystal structure was determined very recently (29). PlsIDH was originally isolated as a catabolic enzyme of L-glucose utilization by P. laeviglucosivorans (30,31). PlsIDH exhibits both sIDH (K m ϭ 3.7 Characterization and structure of levoglucosan dehydrogenase mM and k cat ϭ 11.8 s Ϫ1 ) and L-glucose dehydrogenase (K m ϭ 59.7 mM and k cat ϭ 17.3 s Ϫ1 ) activities (31).…”

Section: Characterization and Structure Of Levoglucosan Dehydrogenasementioning

confidence: 99%

“…PlsIDH was originally isolated as a catabolic enzyme of L-glucose utilization by P. laeviglucosivorans (30,31). PlsIDH exhibits both sIDH (K m ϭ 3.7 Characterization and structure of levoglucosan dehydrogenase mM and k cat ϭ 11.8 s Ϫ1 ) and L-glucose dehydrogenase (K m ϭ 59.7 mM and k cat ϭ 17.3 s Ϫ1 ) activities (31). Subsequent hits were 1,5-anhydro-D-fructose (1,5-AF) reductase (AFR) from Sinorhizobium morelense (SmoAFR) (32), aldose-aldose oxidoreductase (AAOR) from Caulobacter crescentus (CcAAOR) (33), glucose-fructose oxidoreductase (GFOR) from Zymomonas mobilis (ZmGFOR) (34), and AFR from Sinorhizobium meliloti (35).…”

Section: Characterization and Structure Of Levoglucosan Dehydrogenasementioning

confidence: 99%

See 1 more Smart Citation

Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase

Sugiura¹,

Nakahara²,

Yamada

et al. 2018

Journal of Biological Chemistry

View full text Add to dashboard Cite

Levoglucosan is the 1,6-anhydrosugar of d-glucose formed by pyrolysis of glucans and is found in the environment and industrial waste. Two types of microbial levoglucosan metabolic pathways are known. Although the eukaryotic pathway involving levoglucosan kinase has been well-studied, the bacterial pathway involving levoglucosan dehydrogenase (LGDH) has not been well-investigated. Here, we identified and cloned the gene from the bacterium and characterized the recombinant protein. The enzyme exhibited high substrate specificity toward levoglucosan and NAD for the oxidative reaction and was confirmed to be LGDH. LGDH also showed weak activities (∼4%) toward l-sorbose and 1,5-anhydro-d-glucitol. The reverse (reductive) reaction using 3-keto-levoglucosan and NADH exhibited significantly lower and higher values than those of the forward reaction. The crystal structures of LGDH in the apo and complex forms with NADH, NADH + levoglucosan, and NADH + l-sorbose revealed that LGDH has a typical fold of Gfo/Idh/MocA family proteins, similar to those of-inositol dehydrogenase, aldose-aldose oxidoreductase, 1,5-anhydro-d-fructose reductase, and glucose-fructose oxidoreductase. The crystal structures also disclosed that the active site of LGDH is distinct from those of these enzymes. The LGDH active site extensively recognized the levoglucosan molecule with six hydrogen bonds, and the C3 atom of levoglucosan was closely located to the C4 atom of NADH nicotinamide. Our study is the first molecular characterization of LGDH, providing evidence for C3-specific oxidation and representing a starting point for future biotechnological use of LGDH and levoglucosan-metabolizing bacteria.

show abstract

Section: Characterization and Structure Of Levoglucosan Dehydrogenasementioning

confidence: 99%

Section: Characterization and Structure Of Levoglucosan Dehydrogenasementioning

confidence: 99%

Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase

Sugiura¹,

Nakahara²,

Yamada

et al. 2018

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…The alignment results indicated that the DK398 T and DK608 strains were highly similar to P. laeviglucosivorans 43P T (98.54 and 98.62 %) [17], P. litorisediminis GHD-05 T (98.34 and 98.41 %) [18], P.…”

Section: Dna Sequencing Genome Assembly and Analysismentioning

confidence: 99%

Whole-genome sequencing of Paracoccus species isolated from the healthy human eye and description of Paracoccus shanxieyensis sp. nov

Dong

Yang

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

Currently, the genus Paracoccus comprises 76 recognized species. Members of Paracoccus are mostly isolated from environmental, animal, and plant sources. This report describes and proposes a novel species of Paracoccus isolated from clinical specimens of the human ocular surface. We isolated two aerobic, Gram-stain-negative, non-spore-forming, coccoid or short rod-shaped, and non-motile strains (designated DK398T and DK608) from conjunctival sac swabs of two healthy volunteers. The results showed that the strains grew best under the conditions of 28°C, pH 7.0, and 1.0 % (w/v) NaCl. Sequence analysis based on the 16S rRNA gene showed that strains DK398T and DK608 were members of Paracoccus , most similar to Paracoccus laeviglucosivorans 43PT (98.54 and 98.62 %), Paracoccus litorisediminis GHD-05T (98.34 and 98.41 %), and Paracoccus limmosus NB88T (98.21 and 98.29 %). Phenotypic analysis showed that DK398T and DK608 were positive for catalase and oxidase, negative for producing N-acetyl-β-glucosaminic acid, arginine dihydrolase, and β-glucuronidase but positive for leucine arylamidase. The predominant isoprenoid quinone was Q-10, and the major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and an unidentified glycolipid. The major fatty acids (>10%) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The meso-diaminopimelic acid was found in the cell wall peptidoglycan of DK398T. The major cell wall sugars were ribose and galactose. Based on the results of phylogenetic analyses, low (<83.22 %) average nucleotide identity, digital DNA–DNA hybridization (<26.0%), chemotaxonomic analysis, and physiological properties, strain DK398T represents a novel species of the genus Paracoccus , for which the name Paracoccus shanxieyensis sp. nov. is proposed. The type strain is DK398T (=CGMCC 1.17227T=JCM 33719T).

show abstract

“…Subsequently, Sasajima et al purified D-threo-aldose dehydrogenase from Pseudomonas caryophylli , which was capable of oxidizing L-glucose [ 2 ]. Recently, a catabolic pathway that can utilize L-glucose has been discovered in Paracoccus laeviglucosivorans [ 3 ], and the component genes have been cloned and characterized [ 4 ]. This pathway is made up by the combination of genes originating from two independent operons.…”

Section: Introductionmentioning

confidence: 99%

Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification

et al. 2018

Self Cite

View full text Add to dashboard Cite

For about 70 years, L-glucose had been considered non-metabolizable by either mammalian or bacterial cells. Recently, however, an L-glucose catabolic pathway has been discovered in Paracoccus laeviglucosivorans, and the genes responsible cloned. Scyllo-inositol dehydrogenase is involved in the first step in the pathway that oxidizes L-glucose to produce L-glucono-1,5-lactone with concomitant reduction of NAD+ dependent manner. Here, we report the crystal structure of the ternary complex of scyllo-inositol dehydrogenase with NAD+ and L-glucono-1,5-lactone at 1.8 Å resolution. The enzyme adopts a homo-tetrameric structure, similar to those of the inositol dehydrogenase family, and the electron densities of the bound sugar was clearly observed, allowing identification of the residues responsible for interaction with the substrate in the catalytic site. In addition to the conserved catalytic residues (Lys106, Asp191, and His195), another residue, His318, located in the loop region of the adjacent subunit, is involved in substrate recognition. Site-directed mutagenesis confirmed the role of these residues in catalytic activity. We also report the complex structures of the enzyme with myo-inositol and scyllo-inosose. The Arg178 residue located in the flexible loop at the entrance of the catalytic site is also involved in substrate recognition, and plays an important role in accepting both L-glucose and inositols as substrates. On the basis of these structural features, which have not been identified in the known inositol dehydrogenases, and a phylogenetic analysis of IDH family enzymes, we suggest a novel subfamily of the GFO/IDH/MocA family. Since many enzymes in this family have not biochemically characterized, our results could promote to find their activities with various substrates.

show abstract

Paracoccus laeviglucosivorans sp. nov., an l-glucose-utilizing bacterium isolated from soil

Cited by 21 publications

References 31 publications

Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase

Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase

Whole-genome sequencing of Paracoccus species isolated from the healthy human eye and description of Paracoccus shanxieyensis sp. nov

Structural basis of L-glucose oxidation by scyllo-inositol dehydrogenase: Implications for a novel enzyme subfamily classification

Contact Info

Product

Resources

About