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Article ; Online: pH-dependent regulation of an acidophilic

Matoba, Yasuyuki / Oda, Kosuke / Wataeda, Maho / Kanemori, Hina / Matsuo, Koichi

2024 Volume 90, Issue 5, Page(s) e0011824

Abstract: Bacteria have two routes for the l-methionine biosynthesis. In one route called the direct sulfuration pathway, acetylated l-homoserine is directly converted into l-homocysteine. The reaction using H: Importance: In the present study, we can elucidate ...

Abstract	Bacteria have two routes for the l-methionine biosynthesis. In one route called the direct sulfuration pathway, acetylated l-homoserine is directly converted into l-homocysteine. The reaction using H Importance: In the present study, we can elucidate the pH-dependent regulation mechanism of the acidophilic OAHS. The acidophilic feature of the enzyme is caused by the introduction of an acidic residue to the neighborhood of the key acidic residue acting as a switch for the structural interconversion. The strategy may be useful in the field of protein engineering to change the optimal pH of the enzymes. In addition, this study may be useful for the development of antibacterial drugs because the l-methionine synthesis essential for bacteria is inhibited by the OAHS inhibitors. The compounds that can inhibit the interconversion between the open and closed forms of OAHS may become antibacterial drugs.
MeSH term(s)	Lactobacillus plantarum/enzymology ; Lactobacillus plantarum/genetics ; Lactobacillus plantarum/metabolism ; Hydrogen-Ion Concentration ; Bacterial Proteins/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/chemistry ; Carbon-Oxygen Lyases
Chemical Substances	O-acetylhomoserine (thiol)-lyase
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/aem.00118-24
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Article ; Online: Structural Insight into the Interaction of Sendai Virus C Protein with Alix To Stimulate Viral Budding.

Oda, Kosuke / Matoba, Yasuyuki / Sugiyama, Masanori / Sakaguchi, Takemasa

Journal of virology

2021 Volume 95, Issue 19, Page(s) e0081521

Abstract: Sendai virus (SeV), belonging to ... ...

Abstract	Sendai virus (SeV), belonging to the
MeSH term(s)	Amino Acid Sequence ; Animals ; Binding, Competitive ; Calcium-Binding Proteins/chemistry ; Calcium-Binding Proteins/metabolism ; Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/metabolism ; Cell Line ; Crystallography, X-Ray ; Endosomal Sorting Complexes Required for Transport/chemistry ; Endosomal Sorting Complexes Required for Transport/metabolism ; Humans ; Interferon-alpha/genetics ; Interferon-alpha/metabolism ; Interferon-beta/genetics ; Interferon-beta/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Domains ; Sendai virus/chemistry ; Sendai virus/genetics ; Sendai virus/metabolism ; Sendai virus/physiology ; Signal Transduction ; Viral Proteins/chemistry ; Viral Proteins/metabolism ; Virion/physiology ; Virus Release
Chemical Substances	CHMP4A protein, human ; CHMP4B protein, human ; Calcium-Binding Proteins ; Cell Cycle Proteins ; Endosomal Sorting Complexes Required for Transport ; Interferon-alpha ; PDCD6IP protein, human ; Viral Proteins ; nonstructural C protein, Sendai virus ; Interferon-beta (77238-31-4)
Language	English
Publishing date	2021-09-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00815-21
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Article ; Online: Catalytic mechanism of DcsB: Arginase framework used for hydrolyzing its inhibitor.

Oda, Kosuke / Sakaguchi, Takemasa / Matoba, Yasuyuki

Protein science : a publication of the Protein Society

2021 Volume 31, Issue 6, Page(s) e4338

Abstract: DcsB, an enzyme produced from the d-cycloserine biosynthetic gene cluster, displays moderate similarity to arginase in the sequence and three-dimensional structure. Arginase is a ubiquitous enzyme hydrolyzing l-arginine to generate l-ornithine and urea, ... ...

Abstract	DcsB, an enzyme produced from the d-cycloserine biosynthetic gene cluster, displays moderate similarity to arginase in the sequence and three-dimensional structure. Arginase is a ubiquitous enzyme hydrolyzing l-arginine to generate l-ornithine and urea, whereas DcsB hydrolyzes N
MeSH term(s)	Amino Acids ; Arginase/chemistry ; Arginase/genetics ; Arginine/metabolism ; Catalysis ; Kinetics ; Ornithine
Chemical Substances	Amino Acids ; Arginine (94ZLA3W45F) ; Ornithine (E524N2IXA3) ; Arginase (EC 3.5.3.1)
Language	English
Publishing date	2021-05-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4338
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Article ; Online: Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway.

Oda, Kosuke / Sakaguchi, Takemasa / Matoba, Yasuyuki

Proteins

2021 Volume 90, Issue 4, Page(s) 912–918

Abstract: The O-ureidoserine racemase (DcsC) is an enzyme found from the biosynthetic gene cluster of antitubercular agent d-cycloserine. Although DcsC is homologous to diaminopimelate epimerase (DapF) that catalyzes the interconversion between ll- and dl- ... ...

Abstract	The O-ureidoserine racemase (DcsC) is an enzyme found from the biosynthetic gene cluster of antitubercular agent d-cycloserine. Although DcsC is homologous to diaminopimelate epimerase (DapF) that catalyzes the interconversion between ll- and dl-diaminopimelic acid, it specifically catalyzes the interconversion between O-ureido-l-serine and its enantiomer. Here we determined the crystal structure of DcsC at a resolution of 2.12 Å, implicating that the catalytic mechanism of DcsC shares similarity with that of DapF. Comparing the structure of the active center of DcsC to that of DapF, Thr72, Thr198, and Tyr219 of DcsC are likely to be involved in the substrate specificity.
MeSH term(s)	Biosynthetic Pathways ; Crystallography, X-Ray ; Cycloserine/chemistry ; Cycloserine/metabolism ; Multigene Family ; Racemases and Epimerases/genetics ; Racemases and Epimerases/metabolism ; Serine/metabolism
Chemical Substances	Serine (452VLY9402) ; Cycloserine (95IK5KI84Z) ; Racemases and Epimerases (EC 5.1.-)
Language	English
Publishing date	2021-12-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.26290
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Article ; Online: The basicity of an active-site water molecule discriminates between tyrosinase and catechol oxidase activity.

Matoba, Yasuyuki / Oda, Kosuke / Muraki, Yoshimi / Masuda, Taro

International journal of biological macromolecules

2021 Volume 183, Page(s) 1861–1870

Abstract: Tyrosinase (Ty) and catechol oxidase (CO) are members of type-3 copper enzymes. While Ty catalyzes both phenolase and catecholase reactions, CO catalyzes only the latter reaction. In the present study, Ty was found to catalyze the catecholase reaction, ... ...

Abstract	Tyrosinase (Ty) and catechol oxidase (CO) are members of type-3 copper enzymes. While Ty catalyzes both phenolase and catecholase reactions, CO catalyzes only the latter reaction. In the present study, Ty was found to catalyze the catecholase reaction, but hardly the phenolase reaction in the presence of the metallochaperon called "caddie protein (Cad)". The ability of the substrates to dissociate the motif shielding the active-site pocket seems to contribute critically to the substrate specificity of Ty. In addition, a mutation at the N191 residue, which forms a hydrogen bond with a water molecule near the active center, decreased the inherent ratio of phenolase versus catecholase activity. Unlike the wild-type complex, reaction intermediates were not observed when the catalytic reaction toward the Y98 residue of Cad was progressed in the crystalline state. The increased basicity of the water molecule may be necessary to inhibit the proton transfer from the conjugate acid to a hydroxide ion bridging the two copper ions. The deprotonation of the substrate hydroxyl by the bridging hydroxide seems to be significant for the efficient catalytic cycle of the phenolase reaction.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Binding Sites ; Catalysis ; Catalytic Domain ; Catechol Oxidase/chemistry ; Catechol Oxidase/genetics ; Catechol Oxidase/metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Metallochaperones/metabolism ; Models, Molecular ; Monophenol Monooxygenase/chemistry ; Monophenol Monooxygenase/genetics ; Monophenol Monooxygenase/metabolism ; Mutation ; Protein Binding ; Protein Conformation ; Streptomyces/enzymology ; Streptomyces/genetics ; Substrate Specificity ; Water/chemistry
Chemical Substances	Bacterial Proteins ; Metallochaperones ; Water (059QF0KO0R) ; Catechol Oxidase (EC 1.10.3.1) ; Monophenol Monooxygenase (EC 1.14.18.1)
Language	English
Publishing date	2021-06-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2021.05.206
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Article: Cyclization mechanism catalyzed by an ATP‐grasp enzyme essential for d‐cycloserine biosynthesis

Matoba, Yasuyuki / Uda, Narutoshi / Kudo, Mako / Sugiyama, Masanori

FEBS journal. 2020 July, v. 287, no. 13

2020

Abstract: In the biosynthetic pathway of an antitubercular antibiotic d‐cycloserine (d‐CS), O‐ureido‐d‐serine (d‐OUS) is converted to d‐CS. We have previously demonstrated that DcsG, classified into the ATP‐grasp superfamily enzyme, catalyzes the ring formation to ...

Abstract	In the biosynthetic pathway of an antitubercular antibiotic d‐cycloserine (d‐CS), O‐ureido‐d‐serine (d‐OUS) is converted to d‐CS. We have previously demonstrated that DcsG, classified into the ATP‐grasp superfamily enzyme, catalyzes the ring formation to generate d‐CS, which is accompanied by the cleavage of a bond in the urea moiety of d‐OUS to remove a carbamoyl group. Although the general ATP‐grasp enzymes catalyze an ATP‐dependent ligation reaction between two substrates, DcsG catalyzes specifically the generation of an intramolecular covalent bond. In the present study, cyanate was found in the reaction mixture, suggesting that carbamoyl group is eliminated as an isocyanic acid during the reaction. By the crystallographic and mutational investigations of DcsG, we anticipate the residues necessary for the binding of d‐OUS. An acylphosphate intermediate must be bound at the narrow pocket of DcsG in a folded conformation, inducing the bond cleavage and the new bond formation to generate cyanate and d‐CS, respectively. DATABASE: Structural data are available in Protein Data Bank database under the accession number 6JIL.
Keywords	antibiotics ; biochemical pathways ; biosynthesis ; chemical bonding ; cleavage (chemistry) ; cyanates ; databases ; enzymes ; moieties ; urea
Language	English
Dates of publication	2020-07
Size	p. 2763-2778.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15163
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Crystal structure of an N

Oda, Kosuke / Shimotani, Natsuki / Kuroda, Teruo / Matoba, Yasuyuki

Acta crystallographica. Section D, Structural biology

2020 Volume 76, Issue Pt 6, Page(s) 506–514

Abstract: DcsB, one of the enzymes encoded in the D-cycloserine (D-CS) biosynthetic gene cluster, displays a high sequence homology to arginase, which contains two manganese ions in the active site. However, DcsB hydrolyzes ... ...

Abstract	DcsB, one of the enzymes encoded in the D-cycloserine (D-CS) biosynthetic gene cluster, displays a high sequence homology to arginase, which contains two manganese ions in the active site. However, DcsB hydrolyzes N
MeSH term(s)	Amidohydrolases/chemistry ; Amidohydrolases/genetics ; Arginine/analogs & derivatives ; Arginine/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Cycloserine/biosynthesis ; Protein Structure, Tertiary ; Streptomyces/enzymology ; Streptomyces/genetics ; Substrate Specificity
Chemical Substances	Bacterial Proteins ; N(omega)-hydroxyarginine (53054-07-2) ; Arginine (94ZLA3W45F) ; Cycloserine (95IK5KI84Z) ; Amidohydrolases (EC 3.5.-)
Language	English
Publishing date	2020-05-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798320004908
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Article ; Online: Lectins engineered to favor a glycan-binding conformation have enhanced antiviral activity.

Matoba, Yasuyuki / Sato, Yuichiro / Oda, Kosuke / Hatori, Yuta / Morimoto, Kinjiro

The Journal of biological chemistry

2021 Volume 296, Page(s) 100698

Abstract: Homologues of the Oscillatoria agardhii agglutinin (OAA) lectins contain a sequence repeat of ∼66 amino acids, with the number of tandem repeats varying across family members. OAA homologues bind high-mannose glycans on viral surface proteins, thereby ... ...

Abstract	Homologues of the Oscillatoria agardhii agglutinin (OAA) lectins contain a sequence repeat of ∼66 amino acids, with the number of tandem repeats varying across family members. OAA homologues bind high-mannose glycans on viral surface proteins, thereby interfering with viral entry into host cells. As such, OAA homologues have potential utility as antiviral agents, but a more detailed understanding of their structure-function relationships would enable us to develop improved constructs. Here, we determined the X-ray crystal structure of free and glycan-bound forms of Pseudomonas taiwanensis lectin (PTL), an OAA-family lectin consisting of two tandem repeats. Like other OAA-family lectins, PTL exhibited a β-barrel-like structure with two symmetrically positioned glycan-binding sites at the opposite ends of the barrel. Upon glycan binding, the conformation of PTL undergoes a more significant change than expected from previous OAA structural analysis. Moreover, the electron density of the bound glycans suggested that the binding affinities are different at the two binding sites. Next, based on analysis of these structures, we used site-specific mutagenesis to create PTL constructs expected to increase the population with a conformation suitable for glycan binding. The engineered PTLs were examined for their antiviral activity against the influenza virus. Interestingly, some exhibited stronger activity compared with that of the parent PTL. We propose that our approach is effective for the generation of potential microbicides with enhanced antiviral activity.
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Crystallography, X-Ray ; Lectins/chemistry ; Lectins/genetics ; Lectins/metabolism ; Lectins/pharmacology ; Models, Molecular ; Orthomyxoviridae/drug effects ; Polysaccharides/metabolism ; Protein Binding ; Protein Conformation, beta-Strand ; Protein Engineering
Chemical Substances	Antiviral Agents ; Lectins ; Polysaccharides
Language	English
Publishing date	2021-04-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.100698
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Article ; Online: Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis.

Matoba, Yasuyuki / Uda, Narutoshi / Kudo, Mako / Sugiyama, Masanori

The FEBS journal

2019 Volume 287, Issue 13, Page(s) 2763–2778

Abstract: In the biosynthetic pathway of an antitubercular antibiotic d-cycloserine (d-CS), O-ureido-d-serine (d-OUS) is converted to d-CS. We have previously demonstrated that DcsG, classified into the ATP-grasp superfamily enzyme, catalyzes the ring formation to ...

Abstract	In the biosynthetic pathway of an antitubercular antibiotic d-cycloserine (d-CS), O-ureido-d-serine (d-OUS) is converted to d-CS. We have previously demonstrated that DcsG, classified into the ATP-grasp superfamily enzyme, catalyzes the ring formation to generate d-CS, which is accompanied by the cleavage of a bond in the urea moiety of d-OUS to remove a carbamoyl group. Although the general ATP-grasp enzymes catalyze an ATP-dependent ligation reaction between two substrates, DcsG catalyzes specifically the generation of an intramolecular covalent bond. In the present study, cyanate was found in the reaction mixture, suggesting that carbamoyl group is eliminated as an isocyanic acid during the reaction. By the crystallographic and mutational investigations of DcsG, we anticipate the residues necessary for the binding of d-OUS. An acylphosphate intermediate must be bound at the narrow pocket of DcsG in a folded conformation, inducing the bond cleavage and the new bond formation to generate cyanate and d-CS, respectively. DATABASE: Structural data are available in Protein Data Bank database under the accession number 6JIL.
MeSH term(s)	Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Binding Sites ; Biocatalysis ; Biosynthetic Pathways ; Crystallography, X-Ray ; Cyclization ; Cycloserine/biosynthesis ; Ligases/chemistry ; Ligases/genetics ; Ligases/metabolism ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation
Chemical Substances	Adenosine Triphosphate (8L70Q75FXE) ; Cycloserine (95IK5KI84Z) ; Ligases (EC 6.-)
Language	English
Publishing date	2019-12-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15163
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Article ; Online: Two types of phenoloxidases contribute to hemolymph PO activity in spiny Lobster.

Masuda, Taro / Kawauchi, Tatsuki / Yata, Yuya / Matoba, Yasuyuki / Toyohara, Haruhiko

Food chemistry

2018 Volume 260, Page(s) 166–173

Abstract: Phenoloxidases (POs) play a crucial role in melanization of crustaceans. There are at least two types of POs characterized in crustaceans: the conventional type (POα here) that is expressed in hemocytes and POβ, a secreted protein synthesized in the ... ...

Abstract	Phenoloxidases (POs) play a crucial role in melanization of crustaceans. There are at least two types of POs characterized in crustaceans: the conventional type (POα here) that is expressed in hemocytes and POβ, a secreted protein synthesized in the hepatopancreas. We investigated the source of PO activity in the hemolymph of a lobster and determined the kinetic parameters of mono- and di-PO activities. In the lobster hemolymph, POα, which formed a hexamer similar to both POβ and hemocyanin, contributed to PO activity, whereas the amount of POβ was low. Kinetic analyses using purified prophenoloxidase of crustaceans showed that lobster POα has a higher rate constant, while shrimp POβ has higher specificity in both mono- and di-PO reactions, when tyramine and dopamine were employed as substrates. There should be at least two types of PO molecules in crustacean hemolymph, but the dominant PO molecule type varies among species.
MeSH term(s)	Animals ; Catechol Oxidase ; Dopamine/metabolism ; Enzyme Precursors ; Hemocyanins/metabolism ; Hemocytes/enzymology ; Hemolymph/enzymology ; Kinetics ; Monophenol Monooxygenase/metabolism ; Palinuridae/enzymology ; Penaeidae/enzymology ; Species Specificity ; Substrate Specificity ; Tyramine/metabolism
Chemical Substances	Enzyme Precursors ; Hemocyanins (9013-72-3) ; pro-phenoloxidase (EC 1.10.3.-) ; Catechol Oxidase (EC 1.10.3.1) ; Monophenol Monooxygenase (EC 1.14.18.1) ; Dopamine (VTD58H1Z2X) ; Tyramine (X8ZC7V0OX3)
Language	English
Publishing date	2018-03-26
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2018.03.110
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