1X25
 
 | | Crystal Structure of a Member of YjgF Family from Sulfolobus Tokodaii (ST0811) | | Descriptor: | Hypothetical UPF0076 protein ST0811 | | Authors: | Miyakawa, T, Lee, W.C, Hatano, K, Kato, Y, Sawano, Y, Miyazono, K, Nagata, K, Tanokura, M. | | Deposit date: | 2005-04-20 | | Release date: | 2006-02-07 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of the YjgF/YER057c/UK114 family protein from the hyperthermophilic archaeon Sulfolobus tokodaii strain 7
Proteins, 62, 2006
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2EJX
 | | Crystal structure of the hypothetical protein STK_08120 from Sulfolobus tokodaii | | Descriptor: | STK_08120 | | Authors: | Miyakawa, T, Miyazono, K, Sawano, Y, Hatano, K, Nagata, K, Tanokura, M. | | Deposit date: | 2007-03-21 | | Release date: | 2008-03-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.79 Å) | | Cite: | A thermoacidophile-specific protein family, DUF3211, functions as a fatty acid carrier with novel binding mode
J.Bacteriol., 195, 2013
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4WFJ
 | | Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 1.75 angstrom resolution | | Descriptor: | CALCIUM ION, CHLORIDE ION, Cutinase | | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | | Deposit date: | 2014-09-15 | | Release date: | 2014-12-24 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190.
Appl.Microbiol.Biotechnol., 99, 2015
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4WFK
 | | Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-bound state at 2.35 angstrom resolution | | Descriptor: | CALCIUM ION, CHLORIDE ION, Cutinase | | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | | Deposit date: | 2014-09-15 | | Release date: | 2014-12-24 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190.
Appl.Microbiol.Biotechnol., 99, 2015
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4WFI
 | | Crystal structure of PET-degrading cutinase Cut190 S226P mutant in Ca(2+)-free state | | Descriptor: | Cutinase | | Authors: | Miyakawa, T, Mizushima, H, Ohtsuka, J, Oda, M, Kawai, F, Tanokura, M. | | Deposit date: | 2014-09-15 | | Release date: | 2014-12-24 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (1.446 Å) | | Cite: | Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190.
Appl.Microbiol.Biotechnol., 99, 2015
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4XRE
 | | Crystal structure of Gnk2 complexed with mannose | | Descriptor: | Antifungal protein ginkbilobin-2, alpha-D-mannopyranose | | Authors: | Miyakawa, T, Hatano, K, Miyauchi, Y, Suwa, Y, Sawano, Y, Tanokura, M. | | Deposit date: | 2015-01-21 | | Release date: | 2015-02-25 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.597 Å) | | Cite: | A secreted protein with plant-specific cysteine-rich motif functions as a mannose-binding lectin that exhibits antifungal activity.
Plant Physiol., 166, 2014
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7WAF
 | | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS and 4x(beta-Asp-Arg) | | Descriptor: | 4x(beta-Asp-Arg), ARGININE, Cyanophycin synthase, ... | | Authors: | Miyakawa, T, Yang, J, Kawasaki, M, Adachi, N, Fujii, A, Miyauchi, Y, Muramatsu, T, Moriya, T, Senda, T, Tanokura, M. | | Deposit date: | 2021-12-14 | | Release date: | 2022-09-07 | | Last modified: | 2024-11-06 | | Method: | ELECTRON MICROSCOPY (2.52 Å) | | Cite: | Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase.
Nat Commun, 13, 2022
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7WAE
 | | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS, 4x(beta-Asp-Arg), and aspartate | | Descriptor: | 4x(beta-Asp-Arg), ARGININE, ASPARTIC ACID, ... | | Authors: | Miyakawa, T, Yang, J, Kawasaki, M, Adachi, N, Fujii, A, Miyauchi, Y, Muramatsu, T, Moriya, T, Senda, T, Tanokura, M. | | Deposit date: | 2021-12-14 | | Release date: | 2022-09-07 | | Last modified: | 2024-11-20 | | Method: | ELECTRON MICROSCOPY (2.64 Å) | | Cite: | Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase.
Nat Commun, 13, 2022
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3A2E
 | | Crystal structure of ginkbilobin-2, the novel antifungal protein from Ginkgo biloba seeds | | Descriptor: | Ginkbilobin-2 | | Authors: | Miyakawa, T, Miyazono, K, Sawano, Y, Hatano, K, Tanokura, M. | | Deposit date: | 2009-05-13 | | Release date: | 2009-06-02 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.38 Å) | | Cite: | Crystal structure of ginkbilobin-2 with homology to the extracellular domain of plant cysteine-rich receptor-like kinases
Proteins, 77, 2009
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3AK4
 | | Crystal structure of NADH-dependent quinuclidinone reductase from agrobacterium tumefaciens | | Descriptor: | NADH-dependent quinuclidinone reductase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | | Authors: | Miyakawa, T, Kataoka, M, Takeshita, D, Nomoto, F, Nagata, K, Shimizu, S, Tanokura, M. | | Deposit date: | 2010-07-07 | | Release date: | 2011-07-13 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of NADH-dependent quinuclidinone reductase from Agrobacterium tumefaciens
To be Published
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3W9K
 | | Crystal structure of thermoacidophile-specific protein STK_08120 complexed with myristic acid | | Descriptor: | FATTY ACID-BINDING PROTEIN, MYRISTIC ACID | | Authors: | Miyakawa, T, Sawano, Y, Miyazono, K, Miyauchi, Y, Hatano, K, Tanokura, M. | | Deposit date: | 2013-04-05 | | Release date: | 2013-07-17 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | A thermoacidophile-specific protein family, DUF3211, functions as a fatty acid carrier with novel binding mode.
J.Bacteriol., 195, 2013
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2MK4
 | | Solution structure of ORF2 | | Descriptor: | Open reading frame 2 | | Authors: | Miyakawa, T, Kobayashi, H, Tashiro, M, Yamanaka, H, Tanokura, M. | | Deposit date: | 2014-01-24 | | Release date: | 2015-03-25 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structural Basis for Action of the External Chaperone for a Propeptide-deficient Serine Protease from Aeromonas sobria.
J.Biol.Chem., 290, 2015
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7WAC
 | | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) | | Descriptor: | Cyanophycin synthase | | Authors: | Kawasaki, M, Miyakawa, T, Yang, J, Adachi, N, Fujii, A, Miyauchi, Y, Muramatsu, T, Moriya, T, Senda, T, Tanokura, M. | | Deposit date: | 2021-12-14 | | Release date: | 2022-09-07 | | Last modified: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (2.91 Å) | | Cite: | Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase.
Nat Commun, 13, 2022
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7WAD
 | | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS | | Descriptor: | Cyanophycin synthase, MAGNESIUM ION, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER | | Authors: | Kawasaki, M, Miyakawa, T, Yang, J, Adachi, N, Fujii, A, Miyauchi, Y, Muramatsu, T, Moriya, T, Senda, T, Tanokura, M. | | Deposit date: | 2021-12-14 | | Release date: | 2022-09-07 | | Last modified: | 2024-06-26 | | Method: | ELECTRON MICROSCOPY (2.96 Å) | | Cite: | Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase.
Nat Commun, 13, 2022
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8XUF
 | | CDF1 Dof domain in palindromic-bound complex with DNA duplex | | Descriptor: | CDF1, DNA (5'-D(*AP*AP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3'), DNA (5'-D(*TP*TP*CP*AP*TP*AP*AP*AP*GP*TP*AP*TP*AP*CP*TP*TP*TP*AP*TP*G)-3'), ... | | Authors: | Furihata, H, Tanokura, M, Miyakawa, T. | | Deposit date: | 2024-01-12 | | Release date: | 2025-03-12 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural insights into CDF1 accumulation on the CONSTANS promoter via a plant-specific DNA-binding domain to regulate gene expression
To be published
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4TWM
 | | Crystal structure of dioscorin from Dioscorea japonica | | Descriptor: | Dioscorin 5, SULFATE ION | | Authors: | Xue, Y.L, Miyakawa, T, Nakamura, A, Tanokura, M. | | Deposit date: | 2014-07-01 | | Release date: | 2015-04-01 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.11 Å) | | Cite: | Yam Tuber Storage Protein Reduces Plant Oxidants Using the Coupled Reactions as Carbonic Anhydrase and Dehydroascorbate Reductase
Mol Plant, 8, 2015
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4H8N
 | | Crystal structure of conjugated polyketone reductase C2 from candida parapsilosis complexed with NADPH | | Descriptor: | Conjugated polyketone reductase C2, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE | | Authors: | Qin, H.-M, Yamamura, A, Miyakawa, T, Maruoka, S, Ohtsuka, J, Nagata, K, Kataoka, M, Shimizu, S, Tanokura, M. | | Deposit date: | 2012-09-23 | | Release date: | 2013-08-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure of conjugated polyketone reductase from Candida parapsilosis IFO 0708 reveals conformational changes for substrate recognition upon NADPH binding
Appl.Microbiol.Biotechnol., 98, 2014
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5H3E
 | | Crystal structure of mouse isocitrate dehydrogenases 2 K256Q mutant complexed with isocitrate | | Descriptor: | ISOCITRIC ACID, Isocitrate dehydrogenase [NADP], mitochondrial, ... | | Authors: | Xu, Y, Liu, L, Miyakawa, T, Nakamura, A, Tanokura, M. | | Deposit date: | 2016-10-23 | | Release date: | 2017-08-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.21 Å) | | Cite: | Studies on the regulatory mechanism of isocitrate dehydrogenase 2 using acetylation mimics
Sci Rep, 7, 2017
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5H3F
 | | Crystal structure of mouse isocitrate dehydrogenases 2 complexed with isocitrate | | Descriptor: | ISOCITRIC ACID, Isocitrate dehydrogenase [NADP], mitochondrial, ... | | Authors: | Xu, Y, Liu, L, Miyakawa, T, Nakamura, A, Tanokura, M. | | Deposit date: | 2016-10-23 | | Release date: | 2017-08-30 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.29 Å) | | Cite: | Studies on the regulatory mechanism of isocitrate dehydrogenase 2 using acetylation mimics
Sci Rep, 7, 2017
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6JH5
 | | Structure of Marine bacterial laminarinase | | Descriptor: | CALCIUM ION, LamCAT | | Authors: | Yang, J, Xu, Y, Miyakawa, T, Ru, L, Tanokura, M, Long, L. | | Deposit date: | 2019-02-17 | | Release date: | 2019-04-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.54 Å) | | Cite: | Molecular Basis for Substrate Recognition and Catalysis by a Marine Bacterial Laminarinase.
Appl.Environ.Microbiol., 86, 2020
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6JIA
 | | Marine bacterial laminarinase mutant E135A complex with laminaritetraose | | Descriptor: | CALCIUM ION, beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose, laminarinase | | Authors: | Yang, J, Xu, Y, Miyakawa, T, Tanokura, M, Long, L. | | Deposit date: | 2019-02-20 | | Release date: | 2019-05-15 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Molecular Basis for Substrate Recognition and Catalysis by a Marine Bacterial Laminarinase.
Appl.Environ.Microbiol., 86, 2020
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8Y9O
 | | Crystal structure of AtKAI2 in complex with KK181N1 | | Descriptor: | (7-methyl-2,3-dihydroindol-1-yl)-(1,2,3-triazol-1-yl)methanone, Probable esterase KAI2 | | Authors: | Wang, J.W, Miyakawa, T, Asami, T. | | Deposit date: | 2024-02-07 | | Release date: | 2024-12-04 | | Last modified: | 2025-01-15 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Identification and structure-guided development of triazole urea-based selective antagonists of Arabidopsis karrikin signaling.
Nat Commun, 16, 2025
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6JHJ
 | | Structure of Marine bacterial laminarinase mutant-E135A | | Descriptor: | CALCIUM ION, LamCAT | | Authors: | Yang, J, Xu, Y, Miyakawa, T, Tanokura, M, Long, L. | | Deposit date: | 2019-02-18 | | Release date: | 2019-04-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.69 Å) | | Cite: | Molecular Basis for Substrate Recognition and Catalysis by a Marine Bacterial Laminarinase.
Appl.Environ.Microbiol., 86, 2020
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5B0H
 | | CRYSTAL STRUCTURE OF HUMAN LEUKOCYTE CELL-DERIVED CHEMOTAXIN 2 | | Descriptor: | Leukocyte cell-derived chemotaxin-2, SULFATE ION, ZINC ION | | Authors: | Zheng, H, Miyakawa, T, Sawano, Y, Tanokura, M. | | Deposit date: | 2015-10-29 | | Release date: | 2016-07-06 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Crystal Structure of Human Leukocyte Cell-derived Chemotaxin 2 (LECT2) Reveals a Mechanistic Basis of Functional Evolution in a Mammalian Protein with an M23 Metalloendopeptidase Fold
J.Biol.Chem., 291, 2016
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7BQV
 | | Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide | | Descriptor: | 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione, Protein cereblon, SULFATE ION, ... | | Authors: | Furihata, H, Miyauchi, Y, Asano, A, Tanokura, M, Miyakawa, T. | | Deposit date: | 2020-03-25 | | Release date: | 2020-08-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide.
Nat Commun, 11, 2020
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