Evidence map›Paper›PMID 26886583›Full record

ArticlePloS one2016

Functional and Structural Analysis of a β-Glucosidase Involved in β-1,2-Glucan Metabolism in Listeria innocua.

Masahiro Nakajima, Ryuta Yoshida, Akimasa Miyanaga, Koichi Abe, Yuta Takahashi, Naohisa Sugimoto, Hiroyuki Toyoizumi, Hiroyuki Nakai, Motomitsu Kitaoka, Hayao Taguchi

Open access · goldAbstract read
In one paragraph

Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
6.5field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

16 citing papers in PubMed, 40 citations in OpenAlex.

  1. Article
  2. New glycoside hydrolase families of β-1,2-glucanases.Protein science : a publication of the Protein Society · 2025
    Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. A Novel β-Glucosidase FromFrontiers in microbiology · 2021
    Article
  8. Review
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Biochemical and structural analyses of a bacterialThe Journal of biological chemistry · 2017
    Article
  15. Article
  16. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 4 institutions in 1 country.

Masahiro NakajimaDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
Ryuta YoshidaDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
Akimasa MiyanagaDepartment of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.
Koichi AbeDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
Yuta TakahashiGraduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan.
Naohisa SugimotoGraduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan.
Hiroyuki ToyoizumiDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
Hiroyuki NakaiGraduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan.
Motomitsu KitaokaNational Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
Hayao TaguchiDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
Tokyo University of Science · JPNiigata University · JPNational Agriculture and Food Research Organization · JPTokyo Institute of Technology · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Despite the presence of β-1,2-glucan in nature, few β-1,2-glucan degrading enzymes have been reported to date. Recently, the Lin1839 protein from Listeria innocua was identified as a 1,2-β-oligoglucan phosphorylase. Since the adjacent lin1840 gene in the gene cluster encodes a putative glycoside hydrolase family 3 β-glucosidase, we hypothesized that Lin1840 is also involved in β-1,2-glucan dissimilation. Here we report the functional and structural analysis of Lin1840. A recombinant Lin1840 protein (Lin1840r) showed the highest hydrolytic activity toward sophorose (Glc-β-1,2-Glc) among β-1,2-glucooligosaccharides, suggesting that Lin1840 is a β-glucosidase involved in sophorose degradation. The enzyme also rapidly hydrolyzed laminaribiose (β-1,3), but not cellobiose (β-1,4) or gentiobiose (β-1,6) among β-linked gluco-disaccharides. We determined the crystal structures of Lin1840r in complexes with sophorose and laminaribiose as productive binding forms. In these structures, Arg572 forms many hydrogen bonds with sophorose and laminaribiose at subsite +1, which seems to be a key factor for substrate selectivity. The opposite side of subsite +1 from Arg572 is connected to a large empty space appearing to be subsite +2 for the binding of sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) in spite of the higher Km value for sophorotriose than that for sophorose. The conformations of sophorose and laminaribiose are almost the same on the Arg572 side but differ on the subsite +2 side that provides no interaction with a substrate. Therefore, Lin1840r is unable to distinguish between sophorose and laminaribiose as substrates. These results provide the first mechanistic insights into β-1,2-glucooligosaccharide recognition by β-glucosidase.

Indexed as

beta-Glucansbeta-GlucosidaseBinding SitesEnzyme InhibitorsKineticsLigandsListeriaModels, MolecularMutant ProteinsOligosaccharidesProtein ConformationSubstrate Specificitybeta-1,2-glucanbeta-Glucansbeta-GlucosidaseEnzyme InhibitorsLigandsMutant ProteinsOligosaccharides

Identifiers

PMID26886583
PMCPMC4757417
OpenAlexW2285036593

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.