T. Arakawa
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View article: Crystal Structure of <i>Bifidobacterium bifidum</i> Glycoside Hydrolase Family 110 α-Galactosidase Specific for Blood Group B Antigen
Crystal Structure of <i>Bifidobacterium bifidum</i> Glycoside Hydrolase Family 110 α-Galactosidase Specific for Blood Group B Antigen Open
To overcome incompatibility issues and increase the possibility of blood transfusion, technologies that enable efficient conversion of A- and B-type red blood cells to the universal donor O-type is desirable. Although several blood type-co…
View article: Crystal structure of<i>Bifidobacterium bifidum</i>glycoside hydrolase family 110 α-galactosidase specific for blood group B antigen
Crystal structure of<i>Bifidobacterium bifidum</i>glycoside hydrolase family 110 α-galactosidase specific for blood group B antigen Open
To overcome incompatibility issues and increase the possibility of blood transfusion, technologies that enable efficient conversion of A- and B-type red blood cells to the universal donor O-type is desirable. Although several blood type-co…
View article: Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography
Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography Open
View article: Single particle cryo-EM of H. thermophilus chaperonin complex
Single particle cryo-EM of H. thermophilus chaperonin complex Open
View article: Single particle cryo-EM of H. thermoluteolus chaperonin complex
Single particle cryo-EM of H. thermoluteolus chaperonin complex Open
View article: Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism
Protocatechuate hydroxylase is a novel group A flavoprotein monooxygenase with a unique substrate recognition mechanism Open
Para-hydroxybenzoate hydroxylase (PHBH) is a group A flavoprotein monooxygenase that hydroxylates p-hydroxybenzoate to protocatechuate (PCA). Despite intensive studies of Pseudomonas aeruginosa p-hydroxybenzoate hydroxylase (PaPobA), the c…
View article: Author Correction: Identification and characterization of endo-α- exo-α-, and exo-β-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria
Author Correction: Identification and characterization of endo-α- exo-α-, and exo-β-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria Open
View article: Identification and characterization of endo-α-, exo-α-, and exo-β-d-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria
Identification and characterization of endo-α-, exo-α-, and exo-β-d-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria Open
View article: Identification and characterization of endo- and exo-hydrolases cleaving the α- and β-D-arabinofuranosidic bonds of lipoarabinomannan and arabinogalactan of Mycobacteria
Identification and characterization of endo- and exo-hydrolases cleaving the α- and β-D-arabinofuranosidic bonds of lipoarabinomannan and arabinogalactan of Mycobacteria Open
Cell walls of pathogenic and acidophilic bacteria, such as Mycobacterium tuberculosis and Mycobacterium leprae , comprise lipoarabinomannan and arabinogalactan, which are composed of D-arabinose, the enantiomer of the typical l-arabinose f…
View article: Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography
Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography Open
Gum arabic (GA) is widely used as an emulsion stabilizer and edible coating, and consists of a complex carbohydrate moiety with a rhamnosyl-glucuronate group capping the non-reducing ends. Enzymes that can specifically cleave the glycosidi…
View article: Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family
Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family Open
View article: Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family
Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family Open
Gum arabic (GA) is widely used as an emulsion stabilizer and coating in several industrial applications, such as foods and pharmaceuticals. GA contains a complex carbohydrate moiety, and the nonreducing ends of the side chains are often ca…
View article: Biochemical and structural characterization of a novel 4‐ <i>O</i> ‐α‐ <scp>l</scp> ‐rhamnosyl‐β‐ <scp>d</scp> ‐glucuronidase from <i>Fusarium oxysporum</i>
Biochemical and structural characterization of a novel 4‐ <i>O</i> ‐α‐ <span>l</span> ‐rhamnosyl‐β‐ <span>d</span> ‐glucuronidase from <i>Fusarium oxysporum</i> Open
In this study, we have isolated the novel enzyme 4‐ O ‐α‐ l ‐rhamnosyl‐β‐ d ‐glucuronidase (FoBGlcA), which releases α‐ l ‐rhamnosyl (1→4) glucuronic acid from gum arabic (GA), from Fusarium oxysporum 12S culture supernatant, and for the f…
View article: Author response for "Biochemical and structural characterization of a novel 4-O-alpha-l-rhamnosyl-beta-d-glucuronidase from Fusarium oxysporum"
Author response for "Biochemical and structural characterization of a novel 4-O-alpha-l-rhamnosyl-beta-d-glucuronidase from Fusarium oxysporum" Open
View article: Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent β‐<scp>l‐</scp>Arabinofuranosidase Inhibitor
Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent β‐<span>l‐</span>Arabinofuranosidase Inhibitor Open
The recent discovery of zinc‐dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys) 3 (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depe…
View article: Molecular analysis of cyclic α-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway
Molecular analysis of cyclic α-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway Open
Cyclic α-maltosyl-(1→6)-maltose (CMM) is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. Here, we report functional and structural analyses on CMM-binding protein (CMMBP), which is a substrate-binding protein (SBP)…
View article: Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121
Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121 Open
Enzymes acting on α-L-arabinofuranosides have been extensively studied; however, the structures and functions of β-L-arabinofuranosidases are not fully understood. Three enzymes and an ABC transporter in a gene cluster of Bifidobacterium l…
View article: [Review] Enzymes Involved in Levoglucosan Metabolism by Microbes
[Review] Enzymes Involved in Levoglucosan Metabolism by Microbes Open
レボグルコサン(LG)はグルカンの熱分解で生じるグルコースの1,6-アンヒドロ糖であり，LG資化性の真核微生物から得られたLGキナーゼとそれを利用した研究は近年大きな進展がみられた．我々は先行研究をもとに細菌Pseudarthrobacter phenanthrenivoransからLG脱水素酵素(LGDH)を取得しその生化学的性質及び構造と機構を明らかにした．LGDHはLGとNAD+に特異的な活性を示し，3-ケトレボグルコサンを生成する酸化反応を触媒することがわかった．さ…
View article: Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from<i>Sulfurisphaera tokodaii</i>
Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from<i>Sulfurisphaera tokodaii</i> Open
Sulfur oxygenase reductases (SORs) are present in thermophilic and mesophilic archaea and bacteria, and catalyze oxygen-dependent oxygenation and disproportionation of elemental sulfur. SOR has a hollow, spherical homo-24-mer structure and…
View article: Structural analysis of β‐L‐arabinobiose‐binding protein in the metabolic pathway of hydroxyproline‐rich glycoproteins in <i>Bifidobacterium longum</i>
Structural analysis of β‐L‐arabinobiose‐binding protein in the metabolic pathway of hydroxyproline‐rich glycoproteins in <i>Bifidobacterium longum</i> Open
Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for β‐arabinooligosaccharides, which are present in the hydroxyproline‐rich glycoproteins of edible plants. Whereas microbial degradation systems for α…
View article: Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121
Crystal structure of β-L-arabinobiosidase belonging to glycoside hydrolase family 121 Open
Enzymes acting on α-L-arabinofuranosides have been extensively studied; however, the structures and functions of β-L-arabinofuranosidases are not fully understood. Three enzymes and an ABC transporter in a gene cluster of Bifidobacterium l…
View article: Author Correction: Identification and characterization of a novel β-D-galactosidase that releases pyruvylated galactose
Author Correction: Identification and characterization of a novel β-D-galactosidase that releases pyruvylated galactose Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii
Crystallographic and cryogenic electron microscopic structures and enzymatic characterization of sulfur oxygenase reductase from Sulfurisphaera tokodaii Open
View article: Structural basis for the specific cleavage of core-fucosylated N-glycans by endo-β-N-acetylglucosaminidase from the fungus Cordyceps militaris
Structural basis for the specific cleavage of core-fucosylated N-glycans by endo-β-N-acetylglucosaminidase from the fungus Cordyceps militaris Open
View article: Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum
Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum Open
Infant gut-associated bifidobacteria has a metabolic pathway that specifically utilizes lacto- N -biose I (Gal-β1,3-GlcNAc) and galacto- N -biose (Gal-β1,3-GalNAc) from human milk and mucin glycans. UDP-glucose 4-epimerase (GalE) from Bifi…
View article: [Review] Structural Features of Cyclic α-Maltosyl-(1→6)-maltose (CMM) Hydrolase from <i>Arthrobacter </i>Bacteria Critical for CMM Recognition and Hydrolysis
[Review] Structural Features of Cyclic α-Maltosyl-(1→6)-maltose (CMM) Hydrolase from <i>Arthrobacter </i>Bacteria Critical for CMM Recognition and Hydrolysis Open
環状オリゴ糖はその名の通りいくつかの糖が環状に連なったオリゴ糖であり,pHや温度安定性に優れ,非還元性であることから,現在食品のみならず多くの分野で利用されている.環状α-1,6-マルトシルマルトース(CMM)は,四つのグルコースから構成される環状オリゴ糖の一種である.CMMは一般的なα-amylaseでは分解されないが,CMM hydrolase (CMMase)という特殊な酵素によって効率的に分解されることが明らかとなっていた.我々はCMMaseの基質フリーおよび複合体…
View article: Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase
Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase Open
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 involv…
View article: Structural features of a bacterial cyclic α-maltosyl-(1→6)-maltose (CMM) hydrolase critical for CMM recognition and hydrolysis
Structural features of a bacterial cyclic α-maltosyl-(1→6)-maltose (CMM) hydrolase critical for CMM recognition and hydrolysis Open
Cyclic α-maltosyl-(1→6)-maltose (CMM, cyclo-{→6)-α-d-Glcp-(1→4)-α-d-Glcp-(1→6)-α-d-Glcp-(1→4)-α-d-Glcp-(1→})is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. CMM is composed of t…
View article: Identification and characterization of a novel β-D-galactosidase that releases pyruvylated galactose
Identification and characterization of a novel β-D-galactosidase that releases pyruvylated galactose Open
View article: Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell
Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell Open
Colicins are protein toxins produced by and toxic to Escherichia coli strains. Colicin D consists of an N-terminal domain (NTD), central domain (CD) and C-terminal RNase domain (CRD). The cognate immunity protein, ImmD, is co-synthesized i…