北大構造生物学研究室

オートファジーの構造生物学

好中球活性酸素発生系の
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TLR下流のシグナル伝達

インターフェロン産生の
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細胞極性の構造生物学

細胞内シグナル伝達の
構造生物学

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日本核磁気共鳴学会

Home > メンバー > 久米田　博之

		久米田　博之
		北海道大学大学院構造生物学研究室研究員
		kumeta@pharm.hokudai.ac.jp/WEBページ
		理学博士
		イネゲノムに関するタンパク質のNMR mRNA splicingに関するタンパク質のNMR オートファジーに関するタンパク質のNMR を用いた構造生物学

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Kishi K, Kuwatani M, Ohnishi Y, Kumaki Y, Kumeta H, Hirata H, Takishin Y, Furukawa R, Nagai K, Yonemura H, Nozawa S, Sugiura R, Kawakubo K, Aizawa T, Sakamoto N.
Metabolomics of Duodenal Juice for Biliary Tract Cancer Diagnosis.
Cancers (Basel), 15, 4370 (2023)

Taniguchi S, Ono Y, Doi Y, Taniguchi S, Matsuura Y, Iwasaki A, Hirata N, Fukuda R, Inoue K, Yamaguchi M, Tashiro A, Egami D, Aoki S, Kondoh Y, Honda K, Osada H, Kumeta H, Saio T, Okiyoneda T.
Identification of α-Tocopherol succinate as an RFFL-substrate interaction inhibitor inducing peripheral CFTR stabilization and apoptosis.
Biochem Pharmacol, 215, 115730 (2023)

Furukawa A, Shuchi Y, Wang J, Guillen-Poza PA, Ishizuka S, Kagoshima M, Ikeno R, Kumeta H, Yamasaki S, Matsumaru T, Saitoh T, Maenaka K.
Structural basis for plastic glycolipid recognition of the C-type lectin Mincle.
Structure, 31, 1077-1085 (2023)

Song Z, Ohnishi Y, Osada S, Gan L, Jiang J, Hu Z, Kumeta H, Kumaki Y, Yokoi Y, Nakamura K, Ayabe T, Yamauchi K, Aizawa T.
Application of Benchtop NMR for Metabolomics Study Using Feces of Mice with DSS-Induced Colitis.
Metabolites., 13, 611 (2023)

Yanagawa K, Kajikawa A, Sakakibara S, Kumeta H, Tomita H, Matsumoto K.
Real-time NMR analysis of polyhydroxyalkanoate synthase reaction that synthesizes block copolymer comprising glycolate and 3-hydroxybutyrate.
Biophys Chem., 296, 107001 (2023)

Kawagoe S, Kumashiro M, Mabuchi T, Kumeta H, Ishimori K, Saio T.
Heat-Induced Conformational Transition Mechanism of Heat Shock Factor 1 Investigated by Tryptophan Probe.
Biochemistry, 61, 2897-2908 (2022)

Villones LL Jr, Ludwig AK, Kumeta H, Kikuchi S, Ochi R, Aizawa T, Nishimura SI, Gabius HJ, Hinou H.
Exploring the In situ pairing of human galectins toward synthetic O-mannosylated core M1 glycopeptides of α-dystroglycan.
Sci Rep., 12, 17800 (2022)

Gu H, Kato T, Kumeta H, Kumaki Y, Tsukamoto T, Kikukawa T, Demura M, Ishida H, Vogel HJ, Aizawa T.
Three-Dimensional Structure of the Antimicrobial Peptide Cecropin P1 in Dodecylphosphocholine Micelles and the Role of the C-Terminal Residues.
ACS Omega., 7, 31924-31934 (2022)

Kubo K, Watanabe H, Kumeta H, Aizawa T, Seki C, Nakano H, Tokuraku K, Uwai K.
Chemical analysis of amyloid β aggregation inhibitors derived from Geranium thunbergii.
Bioorg Med Chem., 15, 116840 (2022)

Saio T, Hiramatsu S, Asada M, Nakagawa H, Shimizu K, Kumeta H, Nakamura T, Ishimori K.
Conformational ensemble of a multidomain protein explored by Gd3+ electron paramagnetic resonance.
Biophys J., 120, 2943-2951 (2021)

Mimura M, Tomita S, Shinkai Y, Hosokai T, Kumeta H, Saio T, Shiraki K, Kurita R.
Quadruplex Folding Promotes the Condensation of Linker Histones and DNAs via Liquid-Liquid Phase Separation.
J Am Chem Soc., 143, 9849-9857 (2021)

Okumura M, Kanemura S, Matsusaki M, Kinoshita M, Saio T, Ito D, Hirayama C, Kumeta H, Watabe M, Amagai Y, Lee YH, Akiyama S, Inaba K.
A unique leucine-valine adhesive motif supports structure and function of protein disulfide isomerase P5 via dimerization.
Structure, 29, 1357-1370 (2021)

Kawagoe S, Nakagawa H, Kumeta H, Ishimori K, Saio T.
Structural insight into proline cis/trans isomerization of unfolded proteins catalyzed by the trigger factor chaperone.
J Biol Chem, 293, 15095-15106 (2018)

Stewart NJ, Kumeta H, Tomohiro M, Hashimoto T, Hatae N, Matsumoto S.
Long-range heteronuclear J-coupling constants in esters: Implications for 13C metabolic MRI by side-arm parahydrogen-induced polarization.
J Magn Reson., 296, 85-92 (2018)

Kumeta H, Nakayama H, Ogura K.
Solution structure of the major fish allergen parvalbumin Sco j 1 derived from the Pacific mackerel.
Sci Rep., 7, 17160 (2017)

Fukuda N, Noi K, Weng L, Kobashigawa Y, Miyazaki H, Wakeyama Y, Takaki M, Nakahara Y, Tatsuno Y, Uchida-Kamekura M, Suwa Y, Sato T, Ichikawa-Tomikawa N, Nomizu M, Fujiwara Y, Ohsaka F, Saitoh T, Maenaka K, Kumeta H, Shinya S, Kojima C, Ogura T, Morioka H.
Production of Single-Chain Fv Antibodies Specific for GA-Pyridine, an Advanced Glycation End-Product (AGE), with Reduced Inter-Domain Motion.
Molecules, 10, 1695 (2017)

Yoza K, Himeno R, Amano S, Kobashigawa Y, Amemiya S, Fukuda N, Kumeta H, Morioka H, Inagaki F.
Biophysical characterization of drug-resistant mutants of fibroblast growth factor receptor 1.
Genes Cell (2016)

Yamasaki A, Watanabe Y, Adachi W, Suzuki K, Matoba K, Kirisako H, Kumeta H, Nakatogawa H, Ohsumi Y, Inagaki F, Noda NN.
Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates.
Cell Rep., 28, 19-27 (2016)

Kobashigawa Y, Amano S, Yoza K, Himeno R, Amemiya S, Morioka H, Yokogawa M, Kumeta H, Schlessinger J, Inagaki F.
Nuclear magnetic resonance analysis of the conformational state of cancer mutant of fibroblast growth factor receptor 1 tyrosine kinase domain.
Genes Cell, 21, 350-357 (2016)

Yokogawa M, Tsushima T, Noda NN, Kumeta H, Enokizono Y, Yamashita K, Standley DM, Takeuchi O, Akira S, Inagaki F.
Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions.
Sci Rep., 6, 22324 (2016)

Imai M, Saio T, Kumeta H, Uchida T, Inagaki F, Ishimori K.
Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c.
Biochem Biophys Res Commun., 469, 978-984 (2015)

Saio T, Ogura K, Kumeta H, Kobashigawa Y, Shimizu K, Yokochi M, Kodama K, Yamaguchi H, Tsujishita H, Inagaki F
Ligand-driven conformational changes of MurD visualized by paramagnetic NMR.
Sci Rep., 5, 16685 (2015)

Kobashigawa Y, Amano S, Yokogawa M, Kumeta H, Morioka H, Inouye M, Schlessinger J, Inagaki F.
Structural analysis of the mechanism of phosphorylation of a critical autoregulatory tyrosine residue in FGFR1 kinase domain.
Genes Cell, 20, 860-870 (2015)

Kumeta H, Sakakibara H, Enokizono Y, Ogura K, Horiuchi M, Matsumoto M, Seya T, Inagaki F.
The N-terminal domain of TIR domain-containing adaptor molecule-1, TICAM-1.
J Biomol NMR (2014)

Enokizono Y, Kumeta H, Funami K, Horiuchi M, Sarmiento J, Yamashita K, Standley DM, Matsumoto M, Seya T, Inagaki F.
Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling.
Proc Natl Acad Sci U S A. (2013)

Ogura K, Kobashigawa Y, Saio T, Kumeta H, Torikai S, Inagaki F.
Practical applications of hydrostatic pressure to refold proteins from inclusion bodies for NMR structural studies.
Protein Eng Des Sel., 26, 409-416 (2013)

Kumeta H, Ogura K, Nishimiya Y, Miura A, Inagaki F, Tsuda S.
NMR structure note: a defective isoform and its activity-improved variant of a type III antifreeze protein from Zoarces elongates Kner.
J Biomol NMR, 55, 225-230 (2013)

Hayashi T, Senda M, Morohashi H, Higashi H, Horio M, Kashiba Y, Nagase L, Sasaya D, Shimizu T, Venugopalan N, Kumeta H, Noda NN, Inagaki F, Senda T, Hatakeyama M.
Tertiary Structure-Function Analysis Reveals the Pathogenic Signaling Potentiation Mechanism of Helicobacter pylori Oncogenic Effector CagA.
Cell Host Microbe., 12, 20-33 (2012)

Yamaguchi M, Noda NN, Yamamoto H, Shima T, Kumeta H, Kobashigawa Y, Akada R, Ohsumi Y, Inagaki F.
Structural Insights into Atg10-Mediated Formation of the Autophagy-Essential Atg12-Atg5 Conjugate.
Structure, 20, 1244-1254 (2012)

Ogura K, Kumeta H, Takahasi K, Kobashigawa Y, Yoshida R, Itoh H, Yazawa M, Inagaki F.
Solution structures of yeast Saccharomyces cerevisiae calmodulin in calcium- and target peptide-bound states reveal similarities and differences to vertebrate calmodulin.
Genes Cell, 17, 159-172 (2012)

Kobashigawa Y, Tomitaka A, Kumeta H, Noda NN, Yamaguchi M, Inagaki F.
Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b.
Proc Natl Acad Sci U S A., 108, 20579-20584 (2011)

Noda NN, Satoo K, Fujioka Y, Kumeta H, Ogura K, Nakatogawa H, Ohsumi Y, Inagaki F.
Structural basis of Atg8 activation by a homodimeric E1, Atg7.
Mol Cell, 44, 462-475 (2011)

Watanabe Y, Noda NN, Kumeta H, Suzuki K, Ohsumi Y, Inagaki F.
Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by ATG19 and ATG34.
J Biol Chem, 285, 30026-30033 (2010)

Yamaguchi M, Noda NN, Nakatogawa H, Kumeta H, Ohsumi Y, Inagaki F.
Autophagy-related protein (Atg) 8-family interacting motif in Atg3 mediates the Atg3-Atg8 interaction and is crucial for the cytoplasm-to-vacuole targeting pathway.
J Biol Chem, 285, 29599-29607 (2010)

Ogura K, Kumeta H, Inagaki F.
Structure determination of proteins in (2)H (2)O solution aided by a deuterium-decoupled 3D HCA(N)CO experiment.
J Biomol NMR, 47, 243-248 (2010)

Takaku T, Ogura K, Kumeta H, Yoshida N, Inagaki F.
Solution structure of a novel Cdc42-binding module of Bem1 and its interaction with Ste20 and Cdc42.
J Biol Chem, 285, 19346-19353 (2010)

Kumeta H, Watanabe M, Nakatogawa H, Yamaguchi M, Ogura K, Adachi W, Fujioka Y, Noda NN, Ohsumi Y, Inagaki F.
The NMR structure of the autophagy-related protein Atg8.
J Biomol NMR, 47, 237-241 (2010)

Saio T, Yokochi M, Kumeta H, Inagaki F.
PCS-based structure determination of protein-protein complexes.
J Biomol NMR, 46, 271-280 (2010)

Kumeta H, Miwa N, Ogura K, Kai Y, Mizukoshi T, Shimba N, Suzuki EI, Inagaki F.
The NMR structure of protein-glutaminase from Chryseobacterium proteolyticum.
J Biomol NMR, 46, 251-255 (2010)

Takahasi K, Ochiai M, Horiuchi M, Kumeta H, Ogura K, Ashida M, Inagaki F.
Solution structure of the silkworm betaGRP/GNBP3 N-terminal domain reveals the mechanism for beta-1,3-glucan-specific recognition.
Proc Natl Acad Sci U S A., 106, 11679-11684 (2009)

Takahasi K, Kumeta H, Tsuduki N, Narita R, Shigemoto T, Hirai R, Yoneyama M, Horiuchi M, Ogura K, Fujita T, Inagaki F.
Solution structures of cytosolic RNA sensors MDA5 and LGP2 C-terminal domains: Identification of the RNA recognition loop in RIG-I like receptors.
J Biol Chem, 284, 17465-17474 (2009)

Ogura K, Tandai T, Yoshinaga S, Kobashigawa Y, Kumeta H, Ito T, Sumimoto H, Inagaki F.
NMR structure of the heterodimer of Bem1 and Cdc24 PB1 domains from Saccharomyces cerevisiae.
J Biochem (Tokyo), 146, 317-325 (2009)

Kobashigawa Y, Kumeta H, Kanoh D, Inagaki F
The NMR structure of the TC10- and Cdc42-interacting domain of CIP4
J Biomol NMR, 44, 113-118 (2009)

Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F.
The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy
EMBO J, 28, 1341-1350 (2009)

Kobashigawa Y, Kumeta H, Ogura K, Inagaki F.
Attachment of an NMR-invisible solubility enhancement tag using a sortase-mediated protein ligation method.
J Biomol NMR, 43, 145-150 (2009)

Noda NN, Kumeta H, Nakatogawa H, Satoo K, Adachi W, Ishii J, Fujioka Y, Ohsumi Y, Inagaki F.
Structural basis of target recognition by Atg8/LC3 during selective autophagy.
Genes Cell, 13, 1211-1218 (2008)

Kumeta H, Ogura K, Adachi S, Fujioka Y, Tanuma N, Kikuchi K, Inagaki F.
The NMR structure of the NIPP1 FHA domain.
J Biomol NMR, 40, 219-224 (2008)

Takahasi K, Yoneyama M, Nishihori T, Hirai R, Kumeta H, Narita R, Gale M Jr, Inagaki F, Fujita T.
Nonself RNA-Sensing Mechanism of RIG-I Helicase and Activation of Antiviral Immune Responses.
Mol Cell, 29, 428-440 (2008)

Saio T, Kumeta H, Ogura K, Yokochi M, Asayama M, Katoh S, Katoh E, Teshima K, Inagaki F.
The Cooperative Role of OsCnfU-1A Domain I and Domain II in the Iron Sulphur Cluster Transfer Process as Revealed by NMR.
J Biochem (Tokyo), 142, 113-121 (2007)

Kobashigawa Y, Sakai M, Naito M, Yokochi M, Kumeta H, Makino Y, Ogura K, Tanaka S, Inagaki F.
Structural basis for the transforming activity of human cancer-related signaling adaptor protein CRK.
Nat Struct Mol Biol, 14, 503-510 (2007)

Kumeta H, Ogura K, Asayama M, Katoh S, Katoh E, Teshima K, Inagaki F.
The NMR structure of the domain II of a chloroplastic NifU-like protein OsNifU1A.
J Biomol NMR, 38, 161-164 (2007)

Yamada Y, Suzuki NN, Hanada T, Ichimura Y, Kumeta H, Fujioka Y, Ohsumi Y, Inagaki F.
The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation.
J Biol Chem, 282, 8036-8043 (2007)

Katoh S, Murata K, Kubota Y, Kumeta H, Ogura K, Inagaki F, Asayama M, Katoh E.
Refolding and purification of recombinant OsNifU1A domain II that was expressed by Escherichia coli.
Protein Expr Purif, 43, 149-156 (2005)

Kumeta H, Miura A, Kobashigawa Y, Miura K, Oka C, Nemoto N, Nitta K, Tsuda S.
Low-temperature-induced structural changes in human lysozyme elucidated by three-dimensional NMR spectroscopy.
Biochemistry, 42, 1209-1216 (2003)

Kumeta H, Kobashigawa Y, Miura K, Nishimiya Y, Oka C, Nemoto N, Miura A, Nitta K, Tsuda S.
Assignments of 1H, 13C, and 15N resonances of human lysozyme at 4 degrees C.
J Biomol NMR, 22, 183-184 (2002)

Kumeta H, Hoshino T, Goda T, Okayama T, Shimada T, Ohgiya S, Matsuyama H, Ishizaki K.
Identification of a member of the serralysin family isolated from a psychrotrophic bacterium, Pseudomonas fluorescens 114.
Biosci Biotechnol Biochem, 63, 1165-1170 (1999)

Hoshino T, Ishizaki K, Sakamoto T, Kumeta H, Yumoto I, Matsuyama H, Ohgiya S.
Isolation of a Pseudomonas species from fish intestine that produces a protease active at low temperature.
Lett Appl Microbiol, 25, 70-72 (1997)

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