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Nakamura T, Ohyama C, Sakamoto M, Toma T, Tateishi H, Matsuo M, Chirifu M, Ikemizu S, Morioka H, Fujita M, Inoue JI, Yamagata Y. TIFAB regulates the TIFA-TRAF6 signaling pathway involved in innate immunity by forming a heterodimer complex with TIFA. Proc Natl Acad Sci U S A 2024; 121:e2318794121. [PMID: 38442163 PMCID: PMC10945758 DOI: 10.1073/pnas.2318794121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Nuclear factor κB (NF-κB) is activated by various inflammatory and infectious molecules and is involved in immune responses. It has been elucidated that ADP-β-D-manno-heptose (ADP-Hep), a metabolite in gram-negative bacteria, activates NF-κB through alpha-kinase 1 (ALPK1)-TIFA-TRAF6 signaling. ADP-Hep stimulates the kinase activity of ALPK1 for TIFA phosphorylation. Complex formation between phosphorylation-dependent TIFA oligomer and TRAF6 promotes the polyubiquitination of TRAF6 for NF-κB activation. TIFAB, a TIFA homolog lacking a phosphorylation site and a TRAF6 binding motif, is a negative regulator of TIFA-TRAF6 signaling and is implicated in myeloid diseases. TIFAB is indicated to regulate TIFA-TRAF6 signaling through interactions with TIFA and TRAF6; however, little is known about its biological function. We demonstrated that TIFAB forms a complex not with the TIFA dimer, an intrinsic form of TIFA involved in NF-κB activation, but with monomeric TIFA. The structural analysis of the TIFA/TIFAB complex and the biochemical and cell-based analyses showed that TIFAB forms a stable heterodimer with TIFA, inhibits TIFA dimer formation, and suppresses TIFA-TRAF6 signaling. The resultant TIFA/TIFAB complex is a "pseudo-TIFA dimer" lacking the phosphorylation site and TRAF6 binding motif in TIFAB and cannot form the orderly structure as proposed for the phosphorylated TIFA oligomer involved in NF-κB activation. This study elucidated the molecular and structural basis for the regulation of TIFA-TRAF6 signaling by TIFAB.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Chiaki Ohyama
- School of Pharmacy, Kumamoto University, Kumamoto862-0973, Japan
| | - Madoka Sakamoto
- School of Pharmacy, Kumamoto University, Kumamoto862-0973, Japan
| | - Tsugumasa Toma
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Hiroshi Tateishi
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mihoko Matsuo
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mikako Fujita
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Jun-ichiro Inoue
- The University of Tokyo Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), 4-6-1 Shirokanedai, Minato-ku, Tokyo108-0071, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto862-8678, Japan
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Nakamura T, Koga-Ogawa Y, Fujimiya K, Chirifu M, Goto M, Ikemizu S, Nakabeppu Y, Yamagata Y. Protonation states of Asp residues in the human Nudix hydrolase MTH1 contribute to its broad substrate recognition. FEBS Lett 2023. [PMID: 36914375 DOI: 10.1002/1873-3468.14611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023]
Abstract
Human MutT homolog 1 (MTH1), also known as Nudix-type motif 1 (NUDT1), hydrolyzes 8-oxo-dGTP and 2-oxo-dATP with broad substrate recognition and has attracted attention in anticancer therapeutics. Previous studies on MTH1 have proposed that the exchange of the protonation state between Asp119 and Asp120 is essential for the broad substrate recognition of MTH1. To understand the relationship between protonation states and substrate binding, we determined the crystal structures of MTH1 at pH 7.7-9.7. With increasing pH, MTH1 gradually loses its substrate-binding ability, indicating that Asp119 is deprotonated at pH 8.0-9.1 in 8-oxo-dGTP recognition and Asp120 is deprotonated at pH 8.6-9.7 in 2-oxo-dATP recognition. These results confirm that MTH1 recognizes 8-oxo-dGTP and 2-oxo-dATP by exchanging the protonation state between Asp119 and Asp120 with higher pKa .
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Japan
- Priority Organization for Innovation and Excellence, Kumamoto University, Japan
| | - Yukari Koga-Ogawa
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Japan
- Faculty of Health Sciences, Nihon Institute of Medical Science, Saitama, Japan
| | | | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Japan
| | | | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Japan
| | - Yusaku Nakabeppu
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Japan
- Shokei University and Shokei University Junior College, Kumamoto, Japan
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Nakamura T, Yamagata Y. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Proc Natl Acad Sci U S A 2022; 119:e2203118119. [PMID: 35594391 PMCID: PMC9173781 DOI: 10.1073/pnas.2203118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/09/2022] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli MutT prevents mutations by hydrolyzing mutagenic 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) in the presence of Mg2+ or Mn2+ ions. MutT is one of the most studied enzymes in the nucleoside diphosphate-linked moiety X (Nudix) hydrolase superfamily, which is widely distributed in living organisms. However, the catalytic mechanisms of most Nudix hydrolases, including two- or three-metal-ion mechanisms, are still unclear because these mechanisms are proposed using the structures mimicking the reaction states, such as substrate analog complexes. Here, we visualized the hydrolytic reaction process of MutT by time-resolved X-ray crystallography using a biological substrate, 8-oxo-dGTP, and an active metal ion, Mn2+. The reaction was initiated by soaking MutT crystals in a MnCl2 solution and stopped by freezing the crystals at various time points. In total, five types of intermediate structures were refined by investigating the time course of the electron densities in the active site as well as the anomalous signal intensities of Mn2+ ions. The structures and electron densities show that three Mn2+ ions bind to the Nudix motif of MutT and align the substrate 8-oxo-dGTP for catalysis. Accompanied by the coordination of the three Mn2+ ions, a water molecule, bound to a catalytic base, forms a binuclear Mn2+ center for nucleophilic substitution at the β-phosphorus of 8-oxo-dGTP. The reaction condition using Mg2+ also captured a structure in complex with three Mg2+ ions. This study provides the structural details essential for understanding the three-metal-ion mechanism of Nudix hydrolases and proposes that some of the Nudix hydrolases share this mechanism.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto, 862-8678, Japan
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Nakamura T, Okabe K, Hirayama S, Chirifu M, Ikemizu S, Morioka H, Nakabeppu Y, Yamagata Y. Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer. Nucleic Acids Res 2021; 49:7154-7163. [PMID: 34142156 PMCID: PMC8266592 DOI: 10.1093/nar/gkab492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/17/2021] [Accepted: 05/22/2021] [Indexed: 11/17/2022] Open
Abstract
Mammalian MutY homologue (MUTYH) is an adenine DNA glycosylase that excises adenine inserted opposite 8-oxoguanine (8-oxoG). The inherited variations in human MUTYH gene are known to cause MUTYH-associated polyposis (MAP), which is associated with colorectal cancer. MUTYH is involved in base excision repair (BER) with proliferating cell nuclear antigen (PCNA) in DNA replication, which is unique and critical for effective mutation-avoidance. It is also reported that MUTYH has a Zn-binding motif in a unique interdomain connector (IDC) region, which interacts with Rad9–Rad1–Hus1 complex (9–1–1) in DNA damage response, and with apurinic/apyrimidinic endonuclease 1 (APE1) in BER. However, the structural basis for the BER pathway by MUTYH and its interacting proteins is unclear. Here, we determined the crystal structures of complexes between mouse MUTYH and DNA, and between the C-terminal domain of mouse MUTYH and human PCNA. The structures elucidated the repair mechanism for the A:8-oxoG mispair including DNA replication-coupled repair process involving MUTYH and PCNA. The Zn-binding motif was revealed to comprise one histidine and three cysteine residues. The IDC, including the Zn-binding motif, is exposed on the MUTYH surface, suggesting its interaction modes with 9–1–1 and APE1, respectively. The structure of MUTYH explains how MAP mutations perturb MUTYH function.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Kohtaro Okabe
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Shogo Hirayama
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuo-ku, Kumamoto, 862-0973 Kumamoto, Japan.,Shokei University and Shokei University Junior College, 2-6-78, Kuhonji, Chuo-ku, Kumamoto, 862-8678 Kumamoto, Japan
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Yamaguchi Y, Kato K, Ichimaru Y, Jin W, Sakai M, Abe M, Wachino JI, Arakawa Y, Miyagi Y, Imai M, Fukuishi N, Yamagata Y, Otsuka M, Fujita M, Kurosaki H. Crystal Structures of Metallo-β-Lactamase (IMP-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester. J Med Chem 2021; 64:10019-10026. [PMID: 34242022 DOI: 10.1021/acs.jmedchem.1c00308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The emergence and rapid spread of carbapenem-resistant pathogens producing metallo-β-lactamases such as IMP-1 and NDM-1 have been of great concern in the global clinical setting. The X-ray crystal structures of IMP-1 from Serratia marcescens and its single mutant, D120E, in complexes with citrate were determined at resolutions of 2.00 and 1.85 Å, respectively. Two crystal structures indicate that a single mutation at position 120 caused a structural change around Zn1, where the geometry changes from a tetrahedron in the native IMP-1 to a square pyramid in D120E. Based on these two complex structures, the authors synthesized citrate monobenzyl ester 1 to evaluate the structural requirement for the inhibitory activity against IMP-1 and compared the inhibitory activities with nonsubstituted citrate. The introduction of a benzyl group into citrate enhanced the inhibitory activity in comparison to citrate (IC50 > 5 mM).
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Affiliation(s)
- Yoshihiro Yamaguchi
- Environmental Safety Center, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto 860-8555, Japan
| | - Koichi Kato
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan.,Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Yoshimi Ichimaru
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Wanchun Jin
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Misa Sakai
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Miki Abe
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yukina Miyagi
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Masanori Imai
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Nobuyuki Fukuishi
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Drug Discovery, Science Farm Ltd., 1-7-30 Kuhonji, Chuo-ku, Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hiromasa Kurosaki
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
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Kobashigawa Y, Ohara T, Morita K, Toyota Y, Nakamura T, Kotani S, Arimori T, Yamauchi S, Liu C, Kitazaki M, Wakeyama-Miyazaki Y, Suwa Y, Uchida-Kamekura M, Fukuda N, Sato T, Nakajima M, Takagi J, Yamagata Y, Morioka H. Molecular recognition of a single-chain Fv antibody specific for GA-pyridine, an advanced glycation end-product (AGE), elucidated using biophysical techniques and synthetic antigen analogues. J Biochem 2021; 170:379-387. [PMID: 34185078 DOI: 10.1093/jb/mvab056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Advanced glycation end-products (AGEs) are a heterogeneous group of compounds formed by non-enzymatic reaction between reducing-sugar and Arg/Lys in proteins, and are involved in various diabetic complications. GA-pyridine is derived from glycolaldehyde and is one of the most cytotoxic AGEs. Here, we established a single-chain Fv (scFv) antibody against GA-pyridine, 73MuL9-scFv, and examined the details of its specificity and antigen recognition by using various techniques involving biophysics, chemical biology and structural biology. We also synthesized several compounds that differ slightly in regard to the position and number of GA-pyridine substituent groups, and revealed that GA-pyridine was specifically bound to 73MuL9-scFv. Thermodynamic analysis revealed that the association of GA-pyridine to 73MuL9-scFv was an exothermic and enthalpy driven reaction, and thus that the antigen recognition involved multiple specific interactions. Crystallographic analysis of the Fv fragment of 73MuL9-scFv revealed that several CH-π and hydrogen bond interactions took place between the Fv-fragment and GA-pyridine, which was consistent with the results of thermodynamic analysis. Further studies using 73MuL9-scFv as a tool to clarify the relevance of GA-pyridine to diabetic complications are warranted.
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Affiliation(s)
- Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Toshiya Ohara
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Kosuke Morita
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yuya Toyota
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Teruya Nakamura
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, 2-39-1, Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Shunsuke Kotani
- Department of Organic Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Takao Arimori
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Soichiro Yamauchi
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Chenjiang Liu
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Masaya Kitazaki
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yukari Wakeyama-Miyazaki
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yoshiaki Suwa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Makiyo Uchida-Kamekura
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Natsuki Fukuda
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Takashi Sato
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Makoto Nakajima
- Department of Organic Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuriko Yamagata
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
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Nakagawa A, Helliwell JR, Yamagata Y. Diffraction structural biology - an introductory overview. Acta Crystallogr D Struct Biol 2021; 77:278-279. [PMID: 33645530 DOI: 10.1107/s2059798321001613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Atsushi Nakagawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - John R Helliwell
- Department of Chemistry, The University of Manchester, Brunswick Street, Manchester M13 9PL, United Kingdom
| | - Yuriko Yamagata
- Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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Nakamura T, Hashikawa C, Okabe K, Yokote Y, Chirifu M, Toma-Fukai S, Nakamura N, Matsuo M, Kamikariya M, Okamoto Y, Gohda J, Akiyama T, Semba K, Ikemizu S, Otsuka M, Inoue JI, Yamagata Y. Structural analysis of TIFA: Insight into TIFA-dependent signal transduction in innate immunity. Sci Rep 2020; 10:5152. [PMID: 32198460 PMCID: PMC7083832 DOI: 10.1038/s41598-020-61972-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/03/2020] [Indexed: 11/28/2022] Open
Abstract
TRAF-interacting protein with a forkhead-associated (FHA) domain (TIFA), originally identified as an adaptor protein of TRAF6, has recently been shown to be involved in innate immunity, induced by a pathogen-associated molecular pattern (PAMP). ADP-β-D-manno-heptose, a newly identified PAMP, binds to alpha-kinase 1 (ALPK1) and activates its kinase activity to phosphorylate TIFA. Phosphorylation triggers TIFA oligomerisation and formation of a subsequent TIFA-TRAF6 oligomeric complex for ubiquitination of TRAF6, eventually leading to NF-κB activation. However, the structural basis of TIFA-dependent TRAF6 signalling, especially oligomer formation of the TIFA-TRAF6 complex remains unknown. In the present study, we determined the crystal structures of mouse TIFA and two TIFA mutants-Thr9 mutated to either Asp or Glu to mimic the phosphorylation state-to obtain the structural information for oligomer formation of the TIFA-TRAF6 complex. Crystal structures show the dimer formation of mouse TIFA to be similar to that of human TIFA, which was previously reported. This dimeric structure is consistent with the solution structure obtained from small angle X-ray scattering analysis. In addition to the structural analysis, we examined the molecular assembly of TIFA and the TIFA-TRAF6 complex by size-exclusion chromatography, and suggested a model for the TIFA-TRAF6 signalling complex.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan.
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan.
| | - Chie Hashikawa
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kohtaro Okabe
- School of Pharmacy, Kumamoto University, Kumamoto, Japan
| | - Yuya Yokote
- School of Pharmacy, Kumamoto University, Kumamoto, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Sachiko Toma-Fukai
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | | | - Mihoko Matsuo
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan
| | | | - Yoshinari Okamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Masami Otsuka
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun-Ichiro Inoue
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Cellular and Molecular Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
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9
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Koga S, Ikeda S, Akashi R, Yamagata Y, Yonekura T, Kawano H, Maemura K. P6405Potential for drug-drug interaction between vonoprazan and prasugrel on antiplatelet effect assessed by VerifyNow P2Y12 assay in patients with coronary artery disease. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz746.1000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Vonoprazan is a potassium-competitive acid blocker increasingly used in Japan to prevent gastrointestinal bleeding in patients under dual antiplatelet therapy (DAPT) after coronary stents implantation. Since cytochrome P450 (CYP) 3A4 is involved in the primary metabolism of vonoprazan and prasugurel, there is a possibility that CYP-mediated drug-drug interaction between them can attenuate the antiplatelet function of prasugrel.
Purpose
The aim of this study was to investigate whether antiplatelet effect of prasugrel could be attenuated upon coadministration with vonoprazan compared to conventional proton pump inhibitors (PPIs).
Method
We evaluated 72 patients (57 males, 67±11 years) with coronary artery disease who were taking either vonoprazan (n=35) or PPIs (n=37) in combination with DAPT (aspirin and prasugrel) after drug-eluting stents implantation. PPIs included 21 esomeprazole, 8 lansoprazole, and 8 rabeprazole. Antiplatelet effects of prasugrel were assessed using VerifyNow P2Y12 assay. Primary measurements were P2Y12 reaction units (PRU) and P2Y12 percent inhibition. High on-treatment platelet reactivity (HPR) on prasugrel was defined as PRU >208. Administration period of vonoprazan or PPIs in combination with DAPT ≤7 days was defined as early administration period.
Results
Median administration period of vonoprazan or PPIs in combination with DAPT was 127 days. There were no significant differences in baseline clinical characteristics between patients with vonoprazan and PPIs. In the analysis for all subjects, patients with vonoprazan showed similar PRU (166±50 vs. 167±64, p=0.93) and percent inhibition (36±18 vs. 38±23, p=0.66) compared to those with PPIs. No significant differences were observed in the prevalence of HPR between patients with vonoprazan and PPIs (17 vs. 30%, p=0.27). In the analysis for patients in early administration period [vonoprazan (n=14) vs. PPIs (n=10)], there were no significant differences in PRU (166±47 vs. 186±82, p=0.45), percent inhibition (33±17 vs. 30±26, p=0.73), and prevalence of HPR (14 vs. 50%, p=0.085) between patients with vonoprazan and PPIs. In addition, the analysis for patients over early administration period [vonoprazan (n=21) vs. PPIs (n=27)] showed that PRU (166±55 vs. 160±57, p=0.73), percent inhibition (37±19 vs. 41±21, p=0.57), and prevalence of HPR (19 vs. 22%, p=1.00) were comparable between patients with vonoprazan and PPIs.
Conclusion
Compared to PPIs, vonoprazan did not exhibit significant inhibitory effects on the antiplatelet activity of prasugrel assessed by VerifyNow assay. These findings suggest that there are possibly no clinically harmful drug-drug interactions between vonoprazan and prasugrel.
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Affiliation(s)
- S Koga
- Nagasaki University Hospital, Nagasaki, Japan
| | - S Ikeda
- Nagasaki University Hospital, Nagasaki, Japan
| | - R Akashi
- Nagasaki University Hospital, Nagasaki, Japan
| | - Y Yamagata
- Nagasaki University Hospital, Nagasaki, Japan
| | - T Yonekura
- Nagasaki University Hospital, Nagasaki, Japan
| | - H Kawano
- Nagasaki University Hospital, Nagasaki, Japan
| | - K Maemura
- Nagasaki University Hospital, Nagasaki, Japan
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10
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Koga S, Ikeda S, Akashi R, Yamagata Y, Yonekura T, Kawano H, Maemura K. P1549Serum soluble Klotho is associated with extent of coronary artery calcification in patients with stable angina pectoris undergoing percutaneous coronary intervention. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz748.0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Klotho, which was originally identified as an aging suppressor, is a key regulator of bone and mineral metabolism. Transmembrane and soluble forms of Klotho protein have been identified. The transmembrane form serves as an obligate co-receptor for fibroblast growth factor 23 (FGF23). However, the physiological importance of soluble form of Klotho has not been determined.
Purpose
The present study aimed to test the hypothesis that circulating soluble Klotho levels can predict the presence or extent of coronary artery calcification (CAC) in patients with coronary artery disease.
Methods
We analyzed CAC of culprit lesions in patients with 75 stable angina pectoris who were not on dialysis and were scheduled for percutaneous coronary intervention (PCI) following intravascular ultrasound (IVUS). Arc and length of each calcium within the culprit lesion was measured by IVUS. The main outcome measure was the calcium index; a volumetric IVUS-derived measure which was calculated as total calcium length/lesion length × maximal calcium arc/360°. Low calcium index was defined as calcium index <0.042 of the first quartile value. Serum Klotho and FGF23 were measured before PCI. Patients were divided into two groups according to median serum Klotho value: low-Klotho (n=37, ≤460 pg/mL) and high-Klotho group (n=38, >460 pg/mL).
Results
Compared with patients with low-Klotho, those with high-Klotho had higher estimated glomerular filtration rate (eGFR) (69±20 vs. 55±16 mL/min/1.73 m2, p<0.001), lower FGF23 levels (51±24 vs. 67±41 pg/mL, p=0.010). Patients with high-Klotho had significantly lower calcium index than those with low-Klotho (0.17±0.21 vs. 0.24±0.23, p=0.043). Serum Klotho levels correlated significantly and inversely with calcium index (r=−0.31, p=0.006). The correlation between Klotho and calcium index was pronounced at analysis in patients with eGFR <60 mL/min/1.73 m2 (r=−0.52, p<0.001). Logistic regression analysis showed that high-Klotho is a sole significant independent factor associated with low calcium index (odds ratio 7.17, p=0.004). Presence of high-Klotho had high sensitivity and negative predictive value for identifying low calcium index (83% and 92%, respectively).
Conclusions
Serum Klotho values were independently and inversely associated with the degree of CAC assessed by IVUS. These findings have important clinical implications for serum Klotho as a biomarker that reflects the extent of CAC.
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Affiliation(s)
- S Koga
- Nagasaki University Hospital, Nagasaki, Japan
| | - S Ikeda
- Nagasaki University Hospital, Nagasaki, Japan
| | - R Akashi
- Nagasaki University Hospital, Nagasaki, Japan
| | - Y Yamagata
- Nagasaki University Hospital, Nagasaki, Japan
| | - T Yonekura
- Nagasaki University Hospital, Nagasaki, Japan
| | - H Kawano
- Nagasaki University Hospital, Nagasaki, Japan
| | - K Maemura
- Nagasaki University Hospital, Nagasaki, Japan
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11
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Yamagata Y, Ikeda S, Nakata T, Yonekura T, Eguchi M, Koga S, Muroya T, Koide Y, Kawano H, Yao T, Seko Y, Maemura K. P1632Oxidative stress-responsive apoptosis inducing protein (ORAIP), a new oxidative stress marker, is associated with pulmonary hemodynamics in chronic thromboembolic pulmonary hypertension. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p1632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Y Yamagata
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - S Ikeda
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - T Nakata
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - T Yonekura
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - M Eguchi
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - S Koga
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - T Muroya
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - Y Koide
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - H Kawano
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
| | - T Yao
- Institute for Adult Diseases, Division of Cardiovascular Medicine, Tokyo, Japan
| | - Y Seko
- Juntendo University School of Medicine, Department of Biofunctional Microbiota, Tokyo, Japan
| | - K Maemura
- Nagasaki University Hospital, Department of cardiovascular medicine, Nagasaki, Japan
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12
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Koga S, Ikeda S, Akashi R, Yamagata Y, Yonekura T, Muroya T, Koide Y, Kawano H, Maemura K. P5596Circulating soluble Klotho is inversely associated with coronary artery calcification evaluated by three-dimensional intravascular ultrasound. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy566.p5596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- S Koga
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
| | - S Ikeda
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
| | - R Akashi
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
| | - Y Yamagata
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
| | - T Yonekura
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
| | - T Muroya
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
| | - Y Koide
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
| | - H Kawano
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
| | - K Maemura
- Nagasaki University Graduate School of Biomedical Sciences, Department of Cardiovascular Medicine, Nagasaki, Japan
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13
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Hira D, Kitamura R, Nakamura T, Yamagata Y, Furukawa K, Fujii T. Anammox Organism KSU-1 Expresses a Novel His/DOPA Ligated Cytochrome c. J Mol Biol 2018; 430:1189-1200. [DOI: 10.1016/j.jmb.2018.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 10/18/2022]
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14
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Waz S, Nakamura T, Hirata K, Koga-Ogawa Y, Chirifu M, Arimori T, Tamada T, Ikemizu S, Nakabeppu Y, Yamagata Y. Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity. J Biol Chem 2016; 292:2785-2794. [PMID: 28035004 PMCID: PMC5314174 DOI: 10.1074/jbc.m116.749713] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/23/2016] [Indexed: 01/29/2023] Open
Abstract
The human MutT homolog 1 (hMTH1, human NUDT1) hydrolyzes oxidatively damaged nucleoside triphosphates and is the main enzyme responsible for nucleotide sanitization. hMTH1 recently has received attention as an anticancer target because hMTH1 blockade leads to accumulation of oxidized nucleotides in the cell, resulting in mutations and death of cancer cells. Unlike Escherichia coli MutT, which shows high substrate specificity for 8-oxoguanine nucleotides, hMTH1 has broad substrate specificity for oxidized nucleotides, including 8-oxo-dGTP and 2-oxo-dATP. However, the reason for this broad substrate specificity remains unclear. Here, we determined crystal structures of hMTH1 in complex with 8-oxo-dGTP or 2-oxo-dATP at neutral pH. These structures based on high quality data showed that the base moieties of two substrates are located on the similar but not the same position in the substrate binding pocket and adopt a different hydrogen-bonding pattern, and both triphosphate moieties bind to the hMTH1 Nudix motif (i.e. the hydrolase motif) similarly and align for the hydrolysis reaction. We also performed kinetic assays on the substrate-binding Asp-120 mutants (D120N and D120A), and determined their crystal structures in complex with the substrates. Analyses of bond lengths with high-resolution X-ray data and the relationship between the structure and enzymatic activity revealed that hMTH1 recognizes the different oxidized nucleotides via an exchange of the protonation state at two neighboring aspartate residues (Asp-119 and Asp-120) in its substrate binding pocket. To our knowledge, this mechanism of broad substrate recognition by enzymes has not been reported previously and may have relevance for anticancer drug development strategies targeting hMTH1.
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Affiliation(s)
- Shaimaa Waz
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Teruya Nakamura
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973.,the Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto 862-0973
| | - Keisuke Hirata
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Yukari Koga-Ogawa
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Mami Chirifu
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Takao Arimori
- the Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, and
| | - Taro Tamada
- the Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, and
| | - Shinji Ikemizu
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Yusaku Nakabeppu
- the Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuriko Yamagata
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973,
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15
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Mori K, Yamagata Y, Aikou S, Nishida M, Kiyokawa T, Yagi K, Yamashita H, Nomura S, Seto Y. Short-term outcomes of robotic radical esophagectomy for esophageal cancer by a nontransthoracic approach compared with conventional transthoracic surgery. Dis Esophagus 2016; 29:429-34. [PMID: 25809390 PMCID: PMC5132031 DOI: 10.1111/dote.12345] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Transthoracic esophagectomy (TTE) is believed to have advantages for mediastinal lymphadenectomy in the treatment of resectable esophageal cancer despite its association with a greater incidence of pulmonary complications and postoperative mortality. Transhiatal esophagectomy is regarded as less invasive, though insufficient in terms of lymph node dissection. With the aim of achieving lymph dissection equivalent to that of TTE, we have developed a nontransthoracic esophagectomy (NTTE) procedure combining a video-assisted cervical approach for the upper mediastinum and a robot-assisted transhiatal approach for the middle and lower mediastinum. We prospectively studied 22 accumulated cases of NTTE and verified feasibility by analyzing perioperative and histopathological outcomes. We compared this group's short-term outcomes with outcomes of 139 equivalent esophageal cancer cases operated on at our institution by conventional TTE (TTE group). In the NTTE group, there were no procedure-related events and no midway conversions to the conventional surgery; the mean operation time was longer (median, 524 vs. 428 minutes); estimated blood loss did not differ significantly between the two groups (median, 385 mL vs. 490 mL); in the NTTE group, the postoperative hospital stay was shorter (median, 18 days vs. 24 days). No postoperative pneumonia occurred in the NTTE group. The frequencies of other major postoperative complications did not differ significantly, nor were there differences in the numbers of harvested mediastinal lymph nodes (median, 30 vs. 29) or in other histopathology findings. NTTE offers a new radical procedure for resection of esophageal cancer combining a cervical video-assisted approach and a transhiatal robotic approach. Although further accumulation of surgical cases is needed to corroborate these results, NTTE promises better prevention of pulmonary complications in the management of esophageal cancer.
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Affiliation(s)
- K. Mori
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
| | - Y. Yamagata
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
| | - S. Aikou
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
| | - M. Nishida
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
| | - T. Kiyokawa
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
| | - K. Yagi
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
| | - H. Yamashita
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
| | - S. Nomura
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
| | - Y. Seto
- Department of Gastrointestinal SurgeryGraduate School of MedicineUniversity of TokyoTokyoJapan
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16
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Yamaguchi Y, Matsueda S, Matsunaga K, Takashio N, Toma-Fukai S, Yamagata Y, Shibata N, Wachino JI, Shibayama K, Arakawa Y, Kurosaki H. Crystal structure of IMP-2 metallo-β-lactamase from Acinetobacter spp.: comparison of active-site loop structures between IMP-1 and IMP-2. Biol Pharm Bull 2015; 38:96-101. [PMID: 25744464 DOI: 10.1248/bpb.b14-00594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
IMP-2, a subclass B1 metallo-β-lactamase (MBL), is a Zn(II)-containing hydrolase. This hydrolase, involved in antibiotic resistance, catalyzes the hydrolysis of the C-N bond of the β-lactam ring in β-lactam antibiotics such as benzylpenicillin and imipenem. The crystal structure of IMP-2 MBL from Acinetobacter spp. was determined at 2.3 Å resolution. This structure is analogous to that of subclass B1 MBLs such as IMP-1 and VIM-2. Comparison of the structures of IMP-1 and IMP-2, which have an 85% amino acid identity, suggests that the amino acid substitution at position 68 on a β-strand (β3) (Pro in IMP-1 versus Ser in IMP-2) may be a staple factor affecting the flexibility of loop 1 (comprising residues at positions 60-66; EVNGWGV). In the IMP-1 structure, loop 1 adopts an open, disordered conformation. On the other hand, loop 1 of IMP-2 forms a closed conformation in which the side chain of Trp64, involved in substrate binding, is oriented so as to cover the active site, even though there is an acetate ion in the active site of both IMP-1 and IMP-2. Loop 1 of IMP-2 has a more flexible structure in comparison to IMP-1 due to having a Ser residue instead of the Pro residue at position 68, indicating that this difference in sequence may be a trigger to induce a more flexible conformation in loop 1.
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17
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Yoshida S, Yamagata Y, Murayama K, Watanabe K, Imura T, Igarashi Y, Inagaki A, Fujimori K, Ohashi K, Ohuchi N, Satomi S, Goto M. The influence of collagen III expression on the efficiency of cell isolation with the use of collagenase H. Transplant Proc 2015; 46:1942-4. [PMID: 25131077 DOI: 10.1016/j.transproceed.2014.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE We previously demonstrated that collagenase H (ColH) plays a crucial role in rat islet isolation, whereas collagenase G (ColG) plays only a supporting role. We also showed that collagen III appears to be one of the key targets of ColH based on a mass spectrometry analysis. In the present study, we investigated whether our novel findings in an islet isolation model are universally applicable for other types of cell isolation, such as a hepatocyte isolation, with the use of enzyme blends of recombinant collagenases. METHODS As the first step, the expression of one of the main matrix components, collagen III, on rat pancreatic and hepatic tissues was assessed with the use of immunohistochemical staining. ColG and ColH were expressed in recombinant E. coli carrying expression plasmids for each collagenase. Then the efficiency of the collagenase subtype on rat hepatocyte isolation was evaluated in terms of cell yield with the use of thermolysin combined with either ColG or ColH (n = 3, respectively). RESULTS The expression of collagen III on rat hepatic tissues was dramatically lower than that of rat pancreatic tissues. In the rat hepatocyte isolation, a substantial amount of hepatocytes (0.81 ± 0.11 × 10(6)) were obtained in the ColG group, whereas almost no hepatocytes were retrieved in the ColH group, indicating that the influence of the collagenase subtypes in rat hepatocyte isolation are completely opposite to that observed in rat islet isolation. CONCLUSIONS Considering that the expression of collagen III on hepatic tissues was relatively low and that almost no hepatocytes were retrieved when ColH and thermolysin were used, the present study supports our novel finding that collagen III appears to be one of the key targets of ColH in hepatocyte isolation. Therefore, the semiquantification of collagen III on the target tissues not only may positively contribute to efficient islet isolation, but also may affect other types of cell isolation by optimizing the ColH amount.
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Affiliation(s)
- S Yoshida
- Division of Advanced Surgical Science and Technology, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - Y Yamagata
- New Industry Creation Hatchery Center, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan; Department of Applied Biological Chemistry, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - K Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - K Watanabe
- New Industry Creation Hatchery Center, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - T Imura
- New Industry Creation Hatchery Center, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - Y Igarashi
- New Industry Creation Hatchery Center, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - A Inagaki
- New Industry Creation Hatchery Center, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - K Fujimori
- Division of Advanced Surgical Science and Technology, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - K Ohashi
- Department of Surgery, Nara Medical University, Kashihara, Japan
| | - N Ohuchi
- Division of Advanced Surgical Science and Technology, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - S Satomi
- Division of Advanced Surgical Science and Technology, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan
| | - M Goto
- Division of Advanced Surgical Science and Technology, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan; New Industry Creation Hatchery Center, Graduate School of Medical Engineering, Tohoku University, Sendai, Japan.
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18
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Kawai A, Higuchi S, Tsunoda M, Nakamura KT, Yamagata Y, Miyamoto S. Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding. FEBS Lett 2015; 589:2675-82. [PMID: 26318717 DOI: 10.1016/j.febslet.2015.08.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/23/2015] [Accepted: 08/14/2015] [Indexed: 10/23/2022]
Abstract
Uracil-DNA glycosylases (UDGs) excise uracil from DNA by catalyzing the N-glycosidic bond hydrolysis. Here we report the first crystal structures of an archaeal UDG (stoUDG). Compared with other UDGs, stoUDG has a different structure of the leucine-intercalation loop, which is important for DNA binding. The stoUDG-DNA complex model indicated that Leu169, Tyr170, and Asn171 in the loop are involved in DNA intercalation. Mutational analysis showed that Tyr170 is critical for substrate DNA recognition. These results indicate that Tyr170 occupies the intercalation site formed after the structural change of the leucine-intercalation loop required for the catalysis.
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Affiliation(s)
- Akito Kawai
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan.
| | - Shigesada Higuchi
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Masaru Tsunoda
- Faculty of Pharmacy, Iwaki Meisei University, 5-5-1 Chuodai-iino, Iwaki 970-8551, Japan
| | - Kazuo T Nakamura
- School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shuichi Miyamoto
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
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19
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Koketsu S, Sameshima S, Okuyama T, Yamagata Y, Takeshita E, Tagaya N, Oya M. An effective new method for the placement of an anti-adhesion barrier film using an introducer in laparoscopic surgery. Tech Coloproctol 2015; 19:551-3. [PMID: 26165210 DOI: 10.1007/s10151-015-1340-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 06/23/2015] [Indexed: 12/31/2022]
Affiliation(s)
- S Koketsu
- Department of Surgery, Koshigaya Hospital, Dokkyo Medical University, 2-1-50, Minamikoshigaya, Koshigaya City, Saitama, 343-8555, Japan,
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Maekawa R, Sinagawa M, Okada M, Asada H, Taketani T, Yamagata Y, Tamura H, Sugino N, Kubo M. A woman case of familial Mediterranean fever accompanied with periodic fever during menstruation. J Reprod Immunol 2014. [DOI: 10.1016/j.jri.2014.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Nakamura T, Hirata K, Yoshikawa K, Inazato M, Chirifu M, SIkemizu S, Yamagata Y. Kinetic Crystallography on MutT and its homolog. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314095138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Oxidized deoxynucleotides cause replicational errors because of their misincorporations into DNA. The MutT and related proteins prevent transversion mutations by hydrolyzing mutagenic oxidized nucleotides such as 8-oxo-dGTP and 2-oxo-dATP, and there is a difference in substrate specificities between them. E. coli MutT hydrolyzes 8-oxo-dGTP to 8-oxo-dGMP with extremely high substrate specificity. On the other hand, its human homolog has broad substrate specificity for oxidized nucleotides and hydrolyzes 8-oxo-dGTP as well as 2-oxo-dATP. In order to understand mechanisms of their substrate specificities, we solved the crystal structures of MutT and its homolog complexed with their substrates and revealed structural basis of the high substrate specificity of E. coli MutT for 8-oxoguanine nucleotide and the broad substrate specificity of its human honolog for oxidized nucleotides. In this paper, we report the hydrolysis mechanisms of both enzymes revealed by kinetic protein crystallography. Both hydrolysis reactions were initiated by soaking the enzyme-substrate complex crystals in divalent metal solution. After incubation under various conditions, the reactions were terminated by freezing the crystals at 100K. X-ray diffraction data were collected at Spring-8 and Photon Factory. In the MutT crystals, the structures of sequential catalytic intermediates showed the activation mechanism of the nucleophilic water molecule synchronized with the coordination of metal ions. Now by using the crystals of its human homolog, the trial of the catching the intermediate state of catalysis is in progress.
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Chiba Y, Yamagata Y, Nakajima T, Ichishima E. A New High-mannose Type N-Linked Oligosaccharide fromAspergillusCarboxypeptidase. Biosci Biotechnol Biochem 2014; 56:1371-2. [PMID: 1368850 DOI: 10.1271/bbb.56.1371] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Y Chiba
- Department of Applied Biological Chemistry, Faculty of Agriculture, Tohoku University, Sendai, Japan
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Kato T, Yamagata Y, Arai T, Ichishima E. Purification of a New Extracellular 90–kDa Serine Proteinase with Isoelectric Point of 3.9 fromBacillus subtilis(natto) and Elucidation of Its Distinct Mode of Action. Biosci Biotechnol Biochem 2014; 56:1166-8. [PMID: 1368833 DOI: 10.1271/bbb.56.1166] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new extracellular 90-kDa serine proteinase with an isoelectric point (pI) of 3.9 was purified from Bicillus subtilis (natto). Microheterogeneity was detected in the 50-kDa protease of bacillopeptidase F with pI 4.4 reported previously by Wu et al. and the sequence for the first 25 amino acids in the internal region of the enzyme was analyzed: ATDGVEWNVDQIDAPKAWALGYDGA. The cleavage sites in the oxidized B-chain of insulin by the proteinase were CySO3H7-Gly8, Val12-Glu13, Try16-Leu17, and Phe25-Tyr26. The activity was inhibited by phenylmethylsulfonyl fluoride (PMSF) and chymostatin, while the activity was not inhibited by proteinaceous Streptomyces subtilisin inhibitor (SSI) or alpha 2-macroglubulin.
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Affiliation(s)
- T Kato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Tohoku University, Sendai, Japan
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24
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Schuring A, Kiesel L, Gotte M, Cao MZ, Chan RWS, Yeung WSB, Yamagata Y, Asada H, Tamura H, Sugino N, Jin X, Jiang Y, Shen X, Liu H, Zhu L, Shan H, Hu Y, Sun H, Yan G, Tapia-Pizarro A, Archiles S, Argandona F, Devoto L, Miyazaki K, Maruyama T, Masuda H, Oda H, Hida N, Uchida H, Yoshimura Y, Jiang Y, Shen X, Liu H, Zhen X, Sun H, Hu Y, Yan G. Session 59: Endometrium. Hum Reprod 2013. [DOI: 10.1093/humrep/det192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W. Mechanism of the nucleotidyl-transfer reaction in DNA polymerase revealed by time-resolved protein crystallography. Biophysics (Nagoya-shi) 2013; 9:31-6. [PMID: 27493538 PMCID: PMC4629682 DOI: 10.2142/biophysics.9.31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/24/2013] [Indexed: 02/01/2023] Open
Abstract
Nucleotidyl-transfer reaction catalyzed by DNA polymerase is a fundamental enzymatic reaction for DNA synthesis. Until now, a number of structural and kinetic studies on DNA polymerases have proposed a two-metalion mechanism of the nucleotidyl-transfer reaction. However, the actual reaction process has never been visualized. Recently, we have followed the nucleotidyl-transfer reaction process by human DNA polymerase η using time-resolved protein crystallography. In sequence, two Mg2+ ions bind to the active site, the nucleophile 3′-OH is deprotonated, the deoxyribose at the primer end converts from C2′-endo to C3′-endo, and the nucleophile and the α-phosphate of the substrate dATP approach each other to form the new bond. In this process, we observed transient elements, which are a water molecule to deprotonate the 3′-OH and an additional Mg2+ ion to stabilize the intermediate state. Particularly, the third Mg2+ ion observed in this study may be a general feature of the two-metalion mechanism.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan; Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ye Zhao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA; Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Yue-Jin Hua
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Koga Y, Inazato M, Nakamura T, Hashikawa C, Chirifu M, Michi A, Yamashita T, Toma S, Kuniyasu A, Ikemizu S, Nakabeppu Y, Yamagata Y. Crystallization and preliminary X-ray analysis of human MTH1 with a homogeneous N-terminus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 69:45-8. [PMID: 23295485 DOI: 10.1107/s1744309112048002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/21/2012] [Indexed: 11/10/2022]
Abstract
Human MTH1 (hMTH1) is an enzyme that hydrolyses several oxidized purine nucleoside triphosphates to their corresponding nucleoside monophosphates. Crystallographic studies have shown that the accurate mode of interaction between 8-oxoguanine and hMTH1 cannot be understood without determining the positions of the H atoms, as can be observed in neutron and/or ultrahigh-resolution X-ray diffraction studies. The hMTH1 protein prepared in the original expression system from Escherichia coli did not appear to be suitable for obtaining high-quality crystals because the hMTH1 protein had heterogeneous N-termini of Met1 and Gly2 that resulted from N-terminal Met excision by methionine aminopeptidase from the E. coli host. To obtain homogeneous hMTH1, the Gly at the second position was replaced by Lys. As a result, mutant hMTH1 protein [hMTH1(G2K)] with a homogeneous N-terminus could be prepared and high-quality crystals which diffracted to near 1.1 Å resolution using synchrotron radiation were produced. The new crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 46.36, b = 47.58, c = 123.89 Å.
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Affiliation(s)
- Yukari Koga
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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Takagi Y, Setoyama D, Ito R, Kamiya H, Yamagata Y, Sekiguchi M. Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine and deoxyguanosine diphosphates: comparison with MTH1 and MTH2. J Biol Chem 2012; 287:21541-9. [PMID: 22556419 PMCID: PMC3375575 DOI: 10.1074/jbc.m112.363010] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 04/25/2012] [Indexed: 01/25/2023] Open
Abstract
Most of the proteins carrying the 23-residue MutT-related sequence are capable of hydrolyzing compounds with a general structure of nucleoside diphosphate linked to another moiety X and are called the Nudix hydrolases. Among the 22 human Nudix proteins (identified by the sequence signature), some remain uncharacterized as enzymes without a defined substrate. Here, we reveal that the NUDT18 protein, whose substrate was unknown, can degrade 8-oxo-7,8-dihydroguanine (8-oxo-Gua)-containing nucleoside diphosphates to the monophosphates. Because this enzyme is closely related to MTH1 (NUDT1) and MTH2 (NUDT15), we propose that it should be named MTH3. Although these three human proteins resemble each other in their sequences, their substrate specificities differ considerably. MTH1 cleaves 8-oxo-dGTP but not 8-oxo-dGDP, whereas MTH2 can degrade both 8-oxo-dGTP and 8-oxo-dGDP, although the intrinsic enzyme activity of MTH2 is considerably lower than that of MTH1. On the other hand, MTH3 is specifically active against 8-oxo-dGDP and hardly cleaves 8-oxo-dGTP. Other types of oxidized nucleoside diphosphates, 2-hydroxy-dADP and 8-hydroxy-dADP, were also hydrolyzed by MTH3. Another notable feature of the MTH3 enzyme is its action toward the ribonucleotide counterpart. MTH3 can degrade 8-oxo-GDP as efficiently as 8-oxo-dGDP, which is in contrast to the finding that MTH1 and MTH2 show a limited activity against the ribonucleotide counterpart, 8-oxo-GTP. These three enzymes may function together to help maintain the high fidelity of DNA replication and transcription under oxidative stress.
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Affiliation(s)
| | | | - Riyoko Ito
- From the Fukuoka Dental College, Fukuoka 814-0193
| | - Hiroyuki Kamiya
- the Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, and
| | - Yuriko Yamagata
- the Graduate School of Pharmaceutical Science, Kumamoto University, Kumamoto 862-0973, Japan
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Shirouzono T, Chirifu M, Nakamura C, Yamagata Y, Ikemizu S. Preparation, crystallization and preliminary X-ray diffraction studies of the glycosylated form of human interleukin-23. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:432-5. [PMID: 22505413 PMCID: PMC3325813 DOI: 10.1107/s1744309112005295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 02/06/2012] [Indexed: 01/10/2023]
Abstract
Interleukin-23 (IL-23), a member of the IL-12 family, is a heterodimeric cytokine composed of p19 and p40 subunits. IL-23 plays crucial roles in the activation, proliferation and survival of IL-17-producing helper T cells which induce various autoimmune diseases. Human p19 and p40 subunits were cloned and coexpressed in N-acetylglucosaminyltransferase I-negative 293S cells, which produce high-mannose-type glycosylated proteins in order to diminish the heterogeneity of modified N-linked glycans. The glycosylated human IL-23 was purified and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were then collected to 2.6 Å resolution. The crystal belonged to space group P6(1) or P6(5), with unit-cell parameters a = b = 108.94, c = 83.79 Å, γ = 120°. Assuming that the crystal contains one molecule per asymmetric unit, the calculated Matthews coefficient was 2.69 Å(3) Da(-1), with a solvent content of 54.2%. The structure was determined by the molecular-replacement method, with an initial R factor of 52.6%. After subsequent rigid-body and positional refinement, the R(work) and R(free) values decreased to 31.4% and 38.7%, respectively.
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Affiliation(s)
- Takumi Shirouzono
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kummoto 862-0973, Japan
| | - Mami Chirifu
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kummoto 862-0973, Japan
| | - Chiharu Nakamura
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kummoto 862-0973, Japan
| | - Yuriko Yamagata
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kummoto 862-0973, Japan
| | - Shinji Ikemizu
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kummoto 862-0973, Japan
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Wachino JI, Yamaguchi Y, Mori S, Yamagata Y, Arakawa Y, Shibayama K. Crystallization and preliminary X-ray analysis of the subclass B3 metallo-β-lactamase SMB-1 that confers carbapenem resistance. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:343-6. [PMID: 22442240 PMCID: PMC3310548 DOI: 10.1107/s1744309112004691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 02/03/2012] [Indexed: 11/10/2022]
Abstract
The carbapenem-hydrolyzing subclass B3 metallo-β-lactamase SMB-1 was expressed in Escherichia coli and purified. Diffraction data were collected from two types of SMB-1 crystals that were obtained under different conditions. One crystal (SMB-1a) belonged to the trigonal space group P3(1) with unit-cell parameters a = b = 67.83, c = 48.67 Å, while the other crystal (SMB-1b) also belonged to space group P3(1) but with unit-cell parameters a = b = 67.25, c = 46.83 Å. Both crystals contained one molecule per asymmetric unit. Initial phases were determined by molecular replacement; further refinement and model building are in progress.
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Affiliation(s)
- Jun-ichi Wachino
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-Murayama, Tokyo 208-0011, Japan.
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Arimori T, Yamagata Y. [Mechanistic insight into hydrolysis of oxidized nucleotide diphosphates by human NUDT5]. Fukuoka Igaku Zasshi 2011; 102:303-312. [PMID: 22351996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Takao Arimori
- Molecular Structural Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency
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Abe Y, Inoue M, Furuya T, Mukai Y, Nakamura T, Yamagata Y, Nabeshi H, Yoshikawa T, Yoshioka Y, Nagano K, Kamada H, Tsutsumi Y, Tsunoda SI. PS2-054 Biological and structural characterization of human TNFR2-selective TNF mutants. Cytokine 2011. [DOI: 10.1016/j.cyto.2011.07.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yamagata Y, Koga Y, Hashikawa C, Inazato M, Chirifu M, Nakamura T, Ikemizu S, Nakabeppu Y. pH-dependent substrate recognition in human MTH1. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311079840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Suwa Y, Nakamura T, Toma S, Koga T, Shuto T, Ikemizu S, Kai H, Morioka H, Yamagata Y. Structural basis for DNA recognition and binding specificity by the transcription factor Ets2. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311082535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mukai Y, Nakamura T, Yoshikawa M, Yoshioka Y, Tsunoda S, Nakagawa S, Yamagata Y, Tsutsumi Y. Solution of the structure of the TNF-TNFR2 complex. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311092270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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35
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Arimori T, Tamaoki H, Nakamura T, Kamiya H, Ikemizu S, Takagi Y, Ishibashi T, Harashima H, Sekiguchi M, Yamagata Y. Diverse substrate recognition and hydrolysis mechanisms of human NUDT5. Nucleic Acids Res 2011; 39:8972-83. [PMID: 21768126 PMCID: PMC3203587 DOI: 10.1093/nar/gkr575] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Human NUDT5 (hNUDT5) hydrolyzes various modified nucleoside diphosphates including 8-oxo-dGDP, 8-oxo-dADP and ADP-ribose (ADPR). However, the structural basis of the broad substrate specificity remains unknown. Here, we report the crystal structures of hNUDT5 complexed with 8-oxo-dGDP and 8-oxo-dADP. These structures reveal an unusually different substrate-binding mode. In particular, the positions of two phosphates (α and β phosphates) of substrate in the 8-oxo-dGDP and 8-oxo-dADP complexes are completely inverted compared with those in the previously reported hNUDT5–ADPR complex structure. This result suggests that the nucleophilic substitution sites of the substrates involved in hydrolysis reactions differ despite the similarities in the chemical structures of the substrates and products. To clarify this hypothesis, we employed the isotope-labeling method and revealed that 8-oxo-dGDP is attacked by nucleophilic water at Pβ, whereas ADPR is attacked at Pα. This observation reveals that the broad substrate specificity of hNUDT5 is achieved by a diversity of not only substrate recognition, but also hydrolysis mechanisms and leads to a novel aspect that enzymes do not always catalyze the reaction of substrates with similar chemical structures by using the chemically equivalent reaction site.
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Affiliation(s)
- Takao Arimori
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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Ito R, Sekiguchi M, Setoyama D, Nakatsu Y, Yamagata Y, Hayakawa H. Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein. J Biochem 2011; 149:731-8. [PMID: 21389046 DOI: 10.1093/jb/mvr028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MutT-related proteins, including Escherichia coli MutT and the human MTH1 (NUDT1), degrade 8-oxo-7, 8-dihydrodeoxyguanosine triphosphate (8-oxo-dGTP) to 8-oxo-dGMP and thereby prevent mutations caused by the misincorporation of 8-oxoguanine into DNA. The human NUDT5, which has an intrinsic activity to cleave ADP sugars to AMP and sugar phosphate, possesses the ability to degrade 8-oxo-dGDP to the monophosphate. Since 8-oxo-dGDP and 8-oxo-dGTP are interconvertible by cellular enzymes, NUDT5 has the potential to prevent errors during DNA replication. The two activities associated with NUDT5 exhibit different pH dependencies; the optimum for the cleavage of ADP ribose is pH 7-9, while that for 8-oxo-dGDPase is around pH 10. The kinetic parameters for the two types of reactions indicated that ADP ribose is a better substrate for NUDT5 compared with oxidized guanine nucleotides. The 8-oxo-dGDP cleavage was competitively inhibited by ADP ribose and its reaction product, AMP, and in reverse, the cleavage of ADP ribose was inhibited by 8-oxo-dGDP. These results imply that the two types of substrates may share the same binding site for catalysis.
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Affiliation(s)
- Riyoko Ito
- Department of Functional Bioscience and Advanced Science Research Center, Fukuoka Dental College, 2-15-1 Tamura, Sawara-ku, Fukuoka, Japan.
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Nishi K, Ono T, Nakamura T, Fukunaga N, Izumi M, Watanabe H, Suenaga A, Maruyama T, Yamagata Y, Curry S, Otagiri M. Structural insights into differences in drug-binding selectivity between two forms of human alpha1-acid glycoprotein genetic variants, the A and F1*S forms. J Biol Chem 2011; 286:14427-34. [PMID: 21349832 DOI: 10.1074/jbc.m110.208926] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human α(1)-acid glycoprotein (hAGP) in serum functions as a carrier of basic drugs. In most individuals, hAGP exists as a mixture of two genetic variants, the F1*S and A variants, which bind drugs with different selectivities. We prepared a mutant of the A variant, C149R, and showed that its drug-binding properties were indistinguishable from those of the wild type. In this study, we determined the crystal structures of this mutant hAGP alone and complexed with disopyramide (DSP), amitriptyline (AMT), and the nonspecific drug chlorpromazine (CPZ). The crystal structures revealed that the drug-binding pocket on the A variant is located within an eight-stranded β-barrel, similar to that found in the F1*S variant and other lipocalin family proteins. However, the binding region of the A variant is narrower than that of the F1*S variant. In the crystal structures of complexes with DSP and AMT, the two aromatic rings of each drug interact with Phe-49 and Phe-112 at the bottom of the binding pocket. Although the structure of CPZ is similar to those of DSP and AMT, its fused aromatic ring system, which is extended in length by the addition of a chlorine atom, appears to dictate an alternative mode of binding, which explains its nonselective binding to the F1*S and A variant hAGPs. Modeling experiments based on the co-crystal structures suggest that, in complexes of DSP, AMT, or CPZ with the F1*S variant, Phe-114 sterically hinders interactions with DSP and AMT, but not CPZ.
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Affiliation(s)
- Koji Nishi
- Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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Mukai Y, Nakamura T, Yoshikawa M, Yoshioka Y, Tsunoda SI, Nakagawa S, Yamagata Y, Tsutsumi Y. Solution of the structure of the TNF-TNFR2 complex. Sci Signal 2010; 3:ra83. [PMID: 21081755 DOI: 10.1126/scisignal.2000954] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Tumor necrosis factor (TNF) is an inflammatory cytokine that has important roles in various immune responses, which are mediated through its two receptors, TNF receptor 1 (TNFR1) and TNFR2. Antibody-based therapy against TNF is used clinically to treat several chronic autoimmune diseases; however, such treatment sometimes results in serious side effects, which are thought to be caused by the blocking of signals from both TNFRs. Therefore, knowledge of the structural basis for the recognition of TNF by each receptor would be invaluable in designing TNFR-selective drugs. Here, we solved the 3.0 angstrom resolution structure of the TNF-TNFR2 complex, which provided insight into the molecular recognition of TNF by TNFR2. Comparison to the known TNFR1 structure highlighted several differences between the ligand-binding interfaces of the two receptors. Additionally, we also demonstrated that TNF-TNFR2 formed aggregates on the surface of cells, which may be required for signal initiation. These results may contribute to the design of therapeutics for autoimmune diseases.
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Affiliation(s)
- Yohei Mukai
- Laboratory of Biopharmaceutical Research, National Institute of Biomedical Innovation, Osaka, Japan.
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Yamagata Y, Corre G, Joigneaux M, Pariétti V, Galy A, Paldi A. P37. Epigenetic changes induced in human hematopoietic progenitor/stem cells following ex vivo lentiviral transduction. Differentiation 2010. [DOI: 10.1016/j.diff.2010.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Miyata M, Sato T, Kugimiya M, Sho M, Nakamura T, Ikemizu S, Chirifu M, Mizuguchi M, Nabeshima Y, Suwa Y, Morioka H, Arimori T, Suico MA, Shuto T, Sako Y, Momohara M, Koga T, Morino-Koga S, Yamagata Y, Kai H. The Crystal Structure of the Green Tea Polyphenol (−)-Epigallocatechin Gallate−Transthyretin Complex Reveals a Novel Binding Site Distinct from the Thyroxine Binding Site,. Biochemistry 2010; 49:6104-14. [DOI: 10.1021/bi1004409] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masanori Miyata
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Takashi Sato
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Miyuki Kugimiya
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Misato Sho
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | | | | | | | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | | | | | | | - Mary Ann Suico
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Tsuyoshi Shuto
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Yasuhiro Sako
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Mamiko Momohara
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Tomoaki Koga
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Saori Morino-Koga
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | | | - Hirofumi Kai
- Department of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
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Yamaguchi Y, Takashio N, Wachino JI, Yamagata Y, Arakawa Y, Matsuda K, Kurosaki H. Structure of metallo- -lactamase IND-7 from a Chryseobacterium indologenes clinical isolate at 1.65-A resolution. J Biochem 2010; 147:905-15. [DOI: 10.1093/jb/mvq029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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42
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Fujisaki K, Yokota H, Nakatsuchi H, Yamagata Y, Nishikawa T, Udagawa T, Makinouchi A. Observation of three-dimensional internal structure of steel materials by means of serial sectioning with ultrasonic elliptical vibration cutting. J Microsc 2010; 237:89-95. [PMID: 20055922 DOI: 10.1111/j.1365-2818.2009.03306.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A three-dimensional (3D) internal structure observation system based on serial sectioning was developed from an ultrasonic elliptical vibration cutting device and an optical microscope combined with a high-precision positioning device. For bearing steel samples, the cutting device created mirrored surfaces suitable for optical metallography, even for long-cutting distances during serial sectioning of these ferrous materials. Serial sectioning progressed automatically by means of numerical control. The system was used to observe inclusions in steel materials on a scale of several tens of micrometers. Three specimens containing inclusions were prepared from bearing steels. These inclusions could be detected as two-dimensional (2D) sectional images with resolution better than 1 mum. A three-dimensional (3D) model of each inclusion was reconstructed from the 2D serial images. The microscopic 3D models had sharp edges and complicated surfaces.
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Affiliation(s)
- K Fujisaki
- Division of Human Mechanical Systems and Design, Graduate School of Engineering, Hokkaido University, Kita-ku, Sapporo, Japan.
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Nakamura T, Meshitsuka S, Kitagawa S, Abe N, Yamada J, Ishino T, Nakano H, Tsuzuki T, Doi T, Kobayashi Y, Fujii S, Sekiguchi M, Yamagata Y. Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. J Biol Chem 2010; 285:444-52. [PMID: 19864691 PMCID: PMC2804192 DOI: 10.1074/jbc.m109.066373] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 10/14/2009] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli MutT hydrolyzes 8-oxo-dGTP to 8-oxo-dGMP, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in DNA. Of the several enzymes that recognize 8-oxoguanine, MutT exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. The crystal structures of MutT in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dGMP and 8-oxo-dGMP plus Mn(2+), respectively, were determined. MutT strictly recognizes the overall conformation of 8-oxo-dGMP through a number of hydrogen bonds. This recognition mode revealed that 8-oxoguanine nucleotides are discriminated from guanine nucleotides by not only the hydrogen bond between the N7-H and Odelta (N119) atoms but also by the syn glycosidic conformation that 8-oxoguanine nucleotides prefer. Nevertheless, these discrimination factors cannot by themselves explain the roughly 34,000-fold difference between the affinity of MutT for 8-oxo-dGMP and dGMP. When the binary complex of MutT with 8-oxo-dGMP is compared with the ligand-free form, ordering and considerable movement of the flexible loops surrounding 8-oxo-dGMP in the binary complex are observed. These results indicate that MutT specifically recognizes 8-oxoguanine nucleotides by the ligand-induced conformational change.
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Affiliation(s)
- Teruya Nakamura
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
| | - Sachiko Meshitsuka
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Seiju Kitagawa
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Nanase Abe
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Junichi Yamada
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Tetsuya Ishino
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Hiroaki Nakano
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Teruhisa Tsuzuki
- the Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582
| | - Takefumi Doi
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Yuji Kobayashi
- the Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871
| | - Satoshi Fujii
- the School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, and
| | | | - Yuriko Yamagata
- From the Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973
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44
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Matsushita-Morita M, Furukawa I, Suzuki S, Yamagata Y, Koide Y, Ishida H, Takeuchi M, Kashiwagi Y, Kusumoto KI. Characterization of recombinant prolyl aminopeptidase from Aspergillus oryzae. J Appl Microbiol 2009; 109:156-65. [PMID: 20028436 DOI: 10.1111/j.1365-2672.2009.04641.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Prolyl aminopeptidase (PAP) degrades only amino-terminal proline from peptides. The food-grade fungus Aspergillus oryzae produces this enzyme only in small amounts. In this paper, we present efficient production of recombinant PAP with an overexpression system of A. oryzae and characterization of its biochemical properties. METHODS AND RESULTS The gene encoding PAP was overexpressed as a His-tag fusion protein under a taka-amylase gene (amyB) promoter with a limited expressing condition in A. oryzae. The PAP activity in the mycelia grown in rich medium containing glucose (repressing condition) was twice that in starch (inducing condition). The enzyme prepared as cell-free extract was partially purified through two-step column chromatography. The PAP was estimated to be a hexameric protein and exhibited salt tolerance against NaCl of up to 4 mol l(-1). CONCLUSIONS Aspergillus oryzae PAP was produced under the repressing condition of amyB promoter in a PAP-overexpressing strain and purified 1800-folds. Overproduction of PAP under promoter-inducing conditions led to an increase in inactive PAP, possibly because of irregular folding. SIGNIFICANCE AND IMPACT OF THE STUDY PAP with a high specific activity and salt tolerance may be used effectively in the manufacturing processes of fermented foods.
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Miyata M, Sato T, Mizuguchi M, Nakamura T, Ikemizu S, Nabeshima Y, Susuki S, Suwa Y, Morioka H, Ando Y, Suico MA, Shuto T, Koga T, Yamagata Y, Kai H. Role of the Glutamic Acid 54 Residue in Transthyretin Stability and Thyroxine Binding,. Biochemistry 2009; 49:114-23. [DOI: 10.1021/bi901677z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masanori Miyata
- Departments of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Takashi Sato
- Departments of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | | | | | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan
| | - Seiko Susuki
- Departments of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | | | | | - Yukio Ando
- Department of Diagnostic Medicine, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-0811, Japan
| | - Mary Ann Suico
- Departments of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Tsuyoshi Shuto
- Departments of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | - Tomoaki Koga
- Departments of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
| | | | - Hirofumi Kai
- Departments of Molecular Medicine, Global COE Cell Fate Regulation Research and Education Unit
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Kamiya H, Hori M, Arimori T, Sekiguchi M, Yamagata Y, Harashima H. NUDT5 hydrolyzes oxidized deoxyribonucleoside diphosphates with broad substrate specificity. DNA Repair (Amst) 2009; 8:1250-4. [PMID: 19699693 DOI: 10.1016/j.dnarep.2009.07.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/22/2009] [Accepted: 07/27/2009] [Indexed: 01/22/2023]
Abstract
The human NUDT5 protein catalyzes the hydrolysis of 8-hydroxy-dGDP. To examine its substrate specificity, four oxidized deoxyribonucleotides (2-hydroxy-dADP, 8-hydroxy-dADP, 5-formyl-dUDP, and 5-hydroxy-dCDP) were incubated with the NUDT5 protein. Interestingly, all of the nucleotides, except for 5-hydroxy-dCDP, were hydrolyzed with various efficiencies. The kinetic parameters indicated that 8-hydroxy-dADP was hydrolyzed as efficiently as 8-hydroxy-dGDP. The hydrolyzing activities for their triphosphate counterparts were quite weak. These results suggest that the NUDT5 protein eliminates various oxidized deoxyribonucleoside diphosphates from the nucleotide pool and prevents their toxic effects.
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47
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Yamaguchi Y, Sato G, Yamagata Y, Doi Y, Wachino JI, Arakawa Y, Matsuda K, Kurosaki H. Structure of AmpC beta-lactamase (AmpCD) from an Escherichia coli clinical isolate with a tripeptide deletion (Gly286-Ser287-Asp288) in the H10 helix. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:540-3. [PMID: 19478427 DOI: 10.1107/s1744309109014249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 04/16/2009] [Indexed: 11/10/2022]
Abstract
The X-ray crystal structure of AmpC beta-lactamase (AmpC(D)) with a tripeptide deletion (Gly286-Ser287-Asp288) produced by Escherichia coli HKY28, a ceftazidime-resistant strain, was determined at a resolution of 1.7 A. The structure of AmpC(D) suggests that the tripeptide deletion at positions 286-288 located in the H10 helix causes a structural change of the Asn289-Asn294 region from the alpha-helix present in the native AmpC beta-lactamase of E. coli to a loop structure, which results in a widening of the substrate-binding site.
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Mukai Y, Nakamura T, Yoshioka Y, Shibata H, Abe Y, Nomura T, Taniai M, Ohta T, Nakagawa S, Tsunoda SI, Kamada H, Yamagata Y, Tsutsumi Y. Fast binding kinetics and conserved 3D structure underlie the antagonistic activity of mutant TNF: useful information for designing artificial proteo-antagonists. J Biochem 2009; 146:167-72. [PMID: 19386778 DOI: 10.1093/jb/mvp065] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Tumour necrosis factor (TNF) is an important cytokine that induces an inflammatory response predominantly through the TNF receptor-1 (TNFR1). A crucial strategy for the treatment of many autoimmune diseases, therefore, is to block the binding of TNF to TNFR1. We previously identified a TNFR1-selective antagonistic mutant TNF (R1antTNF) from a phage library containing six randomized amino acid residues at the receptor-binding site (amino acids 84-89). Two R1antTNFs, R1antTNF-T2 (A84S, V85T, S86T, Y87H, Q88N and T89Q) and R1antTNF-T8 (A84T, V85P, S86A, Y87I, Q88N and T89R), were successfully isolated from this library. Here, we analysed R1antTNF-T8 using surface plasmon resonance spectroscopy and X-ray crystallography to determine the mechanism underlying the antagonistic activity of R1antTNF. The kinetic association/dissociation parameters of R1antTNF-T8 were higher than those of wild-type TNF, indicating more rapid bond dissociation. X-ray crystallographic analysis suggested that the binding mode of the T89R mutation changed from a hydrophobic to an electrostatic interaction, which may be responsible for the antagonistic behaviour of R1antTNF. Knowledge of these structure-function relationships will facilitate the design of novel TNF inhibitors based on the cytokine structure.
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Mukai Y, Nakamura T, Yoshioka Y, Tsunoda SI, Kamada H, Nakagawa S, Yamagata Y, Tsutsumi Y. Crystallization and preliminary X-ray analysis of the tumour necrosis factor alpha-tumour necrosis factor receptor type 2 complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:295-8. [PMID: 19255488 DOI: 10.1107/s1744309109004461] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/07/2009] [Indexed: 11/11/2022]
Abstract
Tumour necrosis factor receptor type 2 (TNFR2, TNFRSF1B) is an essential receptor for various host-defence functions of tumour necrosis factor alpha (TNF). As part of studies to determine the structure of TNFR2, the formation, crystallization and preliminary X-ray diffraction analysis of the TNF-TNFR2 complex are described. The TNF-TNFR2 complex, which comprises one TNF trimer and three TNFR2 monomers, was confirmed and purified by size-exclusion chromatography. Crystals of the TNF-TNFR2 complex were obtained using polyethylene glycol 3350 as a precipitant. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 74.5, b = 117.4, c = 246.8 A. Assuming the presence of two TNF-TNFR2 complexes in the asymmetric unit, the Matthews coefficient V(M) was 2.49 A(3) Da(-1) and the solvent content of the crystal was 50.7%. The crystal diffracted to 2.95 A resolution.
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50
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Yamagata Y, Maekawa R, Asada H, Taketani T, Tamura I, Tamura H, Ogane J, Hattori N, Shiota K, Sugino N. Aberrant DNA methylation status in human uterine leiomyoma. Mol Hum Reprod 2009; 15:259-67. [DOI: 10.1093/molehr/gap010] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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