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15 results on '"Iizuka, Ippei"'

1. Fragment-based discovery of the first nonpeptidyl inhibitor of dipeptidyl peptidase 11 from Porphyromonas gingivalis

Author

Tanaka, N., primary, Suzuki, Y., additional, Nakamura, A., additional, Watanabe, Y., additional, Sekiya, M., additional, Roppongi, S., additional, Kushibiki, C., additional, Iizuka, Ippei, additional, Tani, O., additional, Sakashita, H., additional, Inaka, K., additional, Tanaka, H., additional, Yamada, M., additional, Ohta, K., additional, Honma, N., additional, Shida, Y., additional, Ogasawara, W., additional, Nakanishi-Matsui, M., additional, Nonaka, T., additional, Gouda, H., additional, and Sakamoto, Y., additional

Published
2023
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2. Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase

Author

Sakamoto, Yasumitsu, Suzuki, Yoshiyuki, Nakamura, Akihiro, Watanabe, Yurie, Sekiya, Mizuki, Roppongi, Saori, Kushibiki, Chisato, Iizuka, Ippei, Tani, Osamu, Sakashita, Hitoshi, Inaka, Koji, Tanaka, Hiroaki, Yamada, Mitsugu, Ohta, Kazunori, Honma, Nobuyuki, Shida, Yosuke, Ogasawara, Wataru, Nakanishi-Matsui, Mayumi, Nonaka, Takamasa, Gouda, Hiroaki, and Tanaka, Nobutada

Published
2019
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4. Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues

Author

Roppongi, Saori, primary, Suzuki, Yoshiyuki, additional, Tateoka, Chika, additional, Fujimoto, Mayu, additional, Morisawa, Saori, additional, Iizuka, Ippei, additional, Nakamura, Akihiro, additional, Honma, Nobuyuki, additional, Shida, Yosuke, additional, Ogasawara, Wataru, additional, Tanaka, Nobutada, additional, Sakamoto, Yasumitsu, additional, and Nonaka, Takamasa, additional

Published
2018
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5. Periplasmic form of dipeptidyl aminopeptidase IV fromPseudoxanthomonas mexicanaWO24: purification, kinetic characterization, crystallization and X-ray crystallographic analysis

Author

Roppongi, Saori, primary, Tateoka, Chika, additional, Fujimoto, Mayu, additional, Iizuka, Ippei, additional, Morisawa, Saori, additional, Nakamura, Akihiro, additional, Honma, Nobuyuki, additional, Suzuki, Yoshiyuki, additional, Shida, Yosuke, additional, Ogasawara, Wataru, additional, Tanaka, Nobutada, additional, Sakamoto, Yasumitsu, additional, and Nonaka, Takamasa, additional

Published
2017
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6. S46 Peptidases are the First Exopeptidases to be Members of Clan PA

Author

中村, 和郎 T., Sakamoto, Yasumitsu, Suzuki, Yoshiyuki, Iizuka, Ippei, Tateoka, Chika, Roppongi, Saori, Fujimoto, Mayu, Inaka, Koji, Tanaka, Hiroaki, Masaki, Mika, Ohta, Kazunori, Okada, Hirofumi, Nonaka, Takamasa, Morikawa, Yasushi, Nakamura, Kazuo T., Ogasawara, Wataru, and Tanaka, Nobutada

Subjects
Molecular Sequence Data, Peptide, Crystallography, X-Ray, Aminopeptidase, Article, Catalysis, Protein Structure, Secondary, Substrate Specificity, Protein structure, Catalytic Domain, Exopeptidases, Hydrolase, Amino Acid Sequence, Dipeptidyl-Peptidases and Tripeptidyl-Peptidases, Peptide sequence, chemistry.chemical_classification, Exopeptidase activity, Multidisciplinary, Chymotrypsin, biology, Hydrogen Bonding, Exopeptidase, Protein Structure, Tertiary, Biochemistry, chemistry, biology.protein
Abstract

The dipeptidyl aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the molecular mechanism of the exopeptidase activity of family S46 peptidase is unknown. Here, we report crystal structures of DAP BII. DAP BII contains a peptidase domain including a typical double b-barrel fold and previously unreported a-helical domain. The structures of peptide complexes revealed that the a-helical domain covers the active-site cleft and the side chain of Asn330 in the domain forms hydrogen bonds with the N-terminus of the bound peptide. These observations indicate that the a-helical domain regulates the exopeptidase activity of DAP BII. Because S46 peptidases are not found in mammals, we expect that our study will be useful for the design of specific inhibitors of S46 peptidases from pathogens., 形態: カラー図版あり, Physical characteristics: Original contains color illustrations, 資料番号: PA1610095000

Published
2014
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7. Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity

Author

Sakamoto, Yasumitsu, Suzuki, Yoshiyuki, Iizuka, Ippei, Tateoka, Chika, Roppongi, Saori, Fujimoto, Mayu, Inaka, Koji, Tanaka, Hiroaki, Yamada, Mitsugu, Ohta, Kazunori, Gouda, Hiroaki, Nonaka, Takamasa, Ogasawara, Wataru, Tanaka, Nobutada, 阪本, 泰光, 鈴木, 義之, 飯塚, 一平, 六本木, 沙織, 伊中, 浩治, 田仲, 広明, 山田, 貢, 太田, 和敬, 合田, 浩明, 野中, 孝昌, 小笠原, 渉, 田中, 信忠, Sakamoto, Yasumitsu, Suzuki, Yoshiyuki, Iizuka, Ippei, Tateoka, Chika, Roppongi, Saori, Fujimoto, Mayu, Inaka, Koji, Tanaka, Hiroaki, Yamada, Mitsugu, Ohta, Kazunori, Gouda, Hiroaki, Nonaka, Takamasa, Ogasawara, Wataru, Tanaka, Nobutada, 阪本, 泰光, 鈴木, 義之, 飯塚, 一平, 六本木, 沙織, 伊中, 浩治, 田仲, 広明, 山田, 貢, 太田, 和敬, 合田, 浩明, 野中, 孝昌, 小笠原, 渉, and 田中, 信忠

Abstract

The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double β-barrel fold and a recently identified regulatory α-helical domain. Crystal structure analyses, docking studies, and biochemical studies revealed that the side chain of Arg673 in the S1 subsite is essential for recognition of the Asp/Glu side chain at the P1 position of the bound substrate. Because S46 peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we anticipate that DPP11s could be utilised as targets for antibiotics. In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms., Physical characteristics: Original contains color illustrations, 形態: カラー図版あり

Published
2016

8. Periplasmic form of dipeptidyl aminopeptidase IV from Pseudoxanthomonas mexicana WO24: purification, kinetic characterization, crystallization and X-ray crystallographic analysis.

Author

Roppongi, Saori, Tateoka, Chika, Fujimoto, Mayu, Iizuka, Ippei, Morisawa, Saori, Nakamura, Akihiro, Honma, Nobuyuki, Suzuki, Yoshiyuki, Shida, Yosuke, Ogasawara, Wataru, Tanaka, Nobutada, Sakamoto, Yasumitsu, and Nonaka, Takamasa

Subjects
AMINOPEPTIDASES, XANTHOMONAS, X-ray crystallography
Abstract

Dipeptidyl aminopeptidase IV (DAP IV or DPP IV) from Pseudoxanthomonas mexicana WO24 (PmDAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position [NH2-P2-P1(Pro/Ala)-P1′-P2′...]. For crystallographic studies, the periplasmic form of PmDAP IV was overproduced in Escherichia coli, purified and crystallized in complex with the tripeptide Lys-Pro-Tyr using the hanging-drop vapour-diffusion method. Kinetic parameters of the purified enzyme against a synthetic substrate were also determined. X-ray diffraction data to 1.90 Å resolution were collected from a triclinic crystal form belonging to space group P1, with unit-cell parameters a = 88.66, b = 104.49, c = 112.84 Å, α = 67.42, β = 68.83, γ = 65.46°. Initial phases were determined by the molecular-replacement method using Stenotrophomonas maltophilia DPP IV (PDB entry ) as a template and refinement of the structure is in progress. [ABSTRACT FROM AUTHOR]

Published
2017
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10. Crystal Structure analyses of dipeptidyl aminopeptidase BII fromP. mexicanaWO24.

Author

Sakamoto, Yasumitsu, primary, Suzuki, Yoshiyuki, additional, Iizuka, Ippei, additional, Tateoka, Chika, additional, Roppongi, Saori, additional, Fujimoto, Mayu, additional, Inaka, Koji, additional, Tanaka, Hiroaki, additional, Ohta, Kazunori, additional, Okada, Hirofumi, additional, Nonaka, Takamasa, additional, Ogasawara, Wataru, additional, and Tanaka, Nobutada, additional

Published
2014
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12. S46 Peptidases are the First Exopeptidases to be Members of Clan PA

Author

Sakamoto, Yasumitsu, primary, Suzuki, Yoshiyuki, additional, Iizuka, Ippei, additional, Tateoka, Chika, additional, Roppongi, Saori, additional, Fujimoto, Mayu, additional, Inaka, Koji, additional, Tanaka, Hiroaki, additional, Masaki, Mika, additional, Ohta, Kazunori, additional, Okada, Hirofumi, additional, Nonaka, Takamasa, additional, Morikawa, Yasushi, additional, Nakamura, Kazuo T., additional, Ogasawara, Wataru, additional, and Tanaka, Nobutada, additional

Published
2014
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13. Crystallization and preliminary X-ray crystallographic studies of dipeptidyl aminopeptidase BII fromPseudoxanthomonas mexicanaWO24

Author

Sakamoto, Yasumitsu, primary, Suzuki, Yoshiyuki, additional, Iizuka, Ippei, additional, Tateoka, Chika, additional, Roppongi, Saori, additional, Okada, Hirofumi, additional, Nonaka, Takamasa, additional, Morikawa, Yasushi, additional, Nakamura, Kazuo T., additional, Ogasawara, Wataru, additional, and Tanaka, Nobutada, additional

Published
2014
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14. Crystallization and preliminary X-ray crystallographic studies of dipeptidyl peptidase 11 from Porphyromonas gingivalis.

Author

Sakamoto, Yasumitsu, Suzuki, Yoshiyuki, Iizuka, Ippei, Tateoka, Chika, Roppongi, Saori, Fujimoto, Mayu, Gouda, Hiroaki, Nonaka, Takamasa, Ogasawara, Wataru, and Tanaka, Nobutada

Subjects
CRYSTALLIZATION, X-ray crystallography, PORPHYROMONAS gingivalis, ESCHERICHIA coli, SPACE groups, WAVELENGTHS
Abstract

Dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) preferentially cleaves substrate peptides with Asp and Glu at the P1 position [NH2-P2-P1(Asp/Glu)-P1′-P2′...]. For crystallographic studies, PgDPP11 was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 1.82 Å resolution were collected from an orthorhombic crystal form belonging to space group C2221, with unit-cell parameters a = 99.33, b = 103.60, c = 177.33 Å. Structural analysis by the multi-wavelength anomalous diffraction method is in progress. [ABSTRACT FROM AUTHOR]

Published
2015
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15. Crystallization and preliminary X-ray crystallographic studies of dipeptidyl aminopeptidase BII from Pseudoxanthomonas mexicana WO24.

Author

Sakamoto, Yasumitsu, Suzuki, Yoshiyuki, Iizuka, Ippei, Tateoka, Chika, Roppongi, Saori, Okada, Hirofumi, Nonaka, Takamasa, Morikawa, Yasushi, Nakamura, Kazuo T., Ogasawara, Wataru, and Tanaka, Nobutada

Subjects
CRYSTALLIZATION, X-ray crystallography, AMINOPEPTIDASES, PEPTIDES, ESCHERICHIA coli
Abstract

Dipeptidyl aminopeptidase BII from Pseudoxanthomonas mexicana WO24 (DAP BII) is able to cleave a variety of dipeptides from the amino-terminus of substrate peptides. For crystallographic studies, DAP BII was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 2.3 Å resolution were collected using an orthorhombic crystal form belonging to space group P212121, with unit-cell parameters a = 76.55, b = 130.86, c = 170.87 Å. Structural analysis by the multi-wavelength anomalous diffraction method is in progress. [ABSTRACT FROM AUTHOR]

Published
2014
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