1AUG
 
 | | CRYSTAL STRUCTURE OF THE PYROGLUTAMYL PEPTIDASE I FROM BACILLUS AMYLOLIQUEFACIENS | | Descriptor: | PYROGLUTAMYL PEPTIDASE-1 | | Authors: | Odagaki, Y, Hayashi, A, Okada, K, Hirotsu, K, Kabashima, T, Ito, K, Yoshimoto, T, Tsuru, D, Sato, M, Clardy, J. | | Deposit date: | 1997-08-26 | | Release date: | 1999-03-23 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | The crystal structure of pyroglutamyl peptidase I from Bacillus amyloliquefaciens reveals a new structure for a cysteine protease.
Structure Fold.Des., 7, 1999
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2HI7
 | | Crystal structure of DsbA-DsbB-ubiquinone complex | | Descriptor: | Disulfide bond formation protein B, Thiol:disulfide interchange protein dsbA, UBIQUINONE-1, ... | | Authors: | Inaba, K, Murakami, S, Suzuki, M, Nakagawa, A, Yamashita, E, Okada, K, Ito, K. | | Deposit date: | 2006-06-29 | | Release date: | 2006-12-05 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | Crystal Structure of the DsbB-DsbA Complex Reveals a Mechanism of Disulfide Bond Generation
Cell(Cambridge,Mass.), 127, 2006
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4U4V
 | | Structure of a nitrate/nitrite antiporter NarK in apo inward-open state | | Descriptor: | NICKEL (II) ION, Nitrate/nitrite transporter NarK, OLEIC ACID | | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | | Deposit date: | 2014-07-24 | | Release date: | 2015-07-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK
Nat Commun, 6, 2015
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4U4W
 | | Structure of a nitrate/nitrite antiporter NarK in nitrate-bound occluded state | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, NITRATE ION, Nitrate/nitrite transporter NarK, ... | | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | | Deposit date: | 2014-07-24 | | Release date: | 2015-07-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK
Nat Commun, 6, 2015
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4U4T
 | | Structure of a nitrate/nitrite antiporter NarK in nitrate-bound inward-open state | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, NITRATE ION, Nitrate/nitrite transporter NarK, ... | | Authors: | Fukuda, M, Takeda, H, Kato, H.E, Doki, S, Ito, K, Maturana, A.D, Ishitani, R, Nureki, O. | | Deposit date: | 2014-07-24 | | Release date: | 2015-07-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK
Nat Commun, 6, 2015
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3J9W
 | | Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex | | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein bS16, ... | | Authors: | Sohmen, D, Chiba, S, Shimokawa-Chiba, N, Innis, C.A, Berninghausen, O, Beckmann, R, Ito, K, Wilson, D.N. | | Deposit date: | 2015-03-16 | | Release date: | 2015-04-29 | | Last modified: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Nat Commun, 6, 2015
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1X3U
 | | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot | | Descriptor: | Transcriptional regulatory protein fixJ | | Authors: | Kurashima-Ito, K, Kasai, Y, Hosono, K, Tamura, K, Oue, S, Isogai, M, Ito, Y, Nakamura, H, Shiro, Y. | | Deposit date: | 2005-05-10 | | Release date: | 2006-05-02 | | Last modified: | 2022-03-02 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium meliloti and its recognition of the fixK promoter
Biochemistry, 44, 2005
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2IPC
 | | Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer | | Descriptor: | Preprotein translocase SecA subunit | | Authors: | Vassylyev, D.G, Mori, H, Vassylyeva, M.N, Tsukazaki, T, Kimura, Y, Tahirov, T.H, Ito, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2006-10-12 | | Release date: | 2006-11-28 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal Structure of the Translocation ATPase SecA from Thermus thermophilus Reveals a Parallel, Head-to-Head Dimer.
J.Mol.Biol., 364, 2006
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5B3S
 | | Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K) | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Shimada, A, Shinzawa-Ito, K, Yoshikawa, S, Tsukihara, T. | | Deposit date: | 2016-03-11 | | Release date: | 2017-03-22 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)
To Be Published
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1IRE
 | | Crystal Structure of Co-type nitrile hydratase from Pseudonocardia thermophila | | Descriptor: | COBALT (II) ION, Nitrile Hydratase | | Authors: | Miyanaga, A, Fushinobu, S, Ito, K, Wakagi, T. | | Deposit date: | 2001-10-01 | | Release date: | 2002-10-01 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure of cobalt-containing nitrile hydratase.
Biochem.Biophys.Res.Commun., 288, 2001
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1EH1
 | | RIBOSOME RECYCLING FACTOR FROM THERMUS THERMOPHILUS | | Descriptor: | RIBOSOME RECYCLING FACTOR | | Authors: | Toyoda, T, Tin, O.F, Ito, K, Fujiwara, T, Kumasaka, T, Yamamoto, M, Garber, M.B, Nakamura, Y. | | Deposit date: | 2000-02-18 | | Release date: | 2000-11-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch.
RNA, 6, 2000
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5AWH
 | | Rhodobacter sphaeroides Argonaute in complex with guide RNA/target DNA heteroduplex | | Descriptor: | DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3'), MAGNESIUM ION, RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3'), ... | | Authors: | Miyoshi, T, Ito, K, Murakami, R, Uchiumi, T. | | Deposit date: | 2015-07-03 | | Release date: | 2016-07-06 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute.
Nat Commun, 7, 2016
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5FG3
 | | Crystal structure of GDP-bound aIF5B from Aeropyrum pernix | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Probable translation initiation factor IF-2 | | Authors: | Murakami, R, Miyoshi, T, Uchiumi, T, Ito, K. | | Deposit date: | 2015-12-20 | | Release date: | 2016-05-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix.
Proteins, 84, 2016
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1J2T
 | | Creatininase Mn | | Descriptor: | MANGANESE (II) ION, SULFATE ION, ZINC ION, ... | | Authors: | Yoshimoto, T, Tanaka, N, Kanada, N, Inoue, T, Nakajima, Y, Haratake, M, Nakamura, K.T, Xu, Y, Ito, K. | | Deposit date: | 2003-01-11 | | Release date: | 2004-01-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
J.Mol.Biol., 337, 2004
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1J2U
 | | Creatininase Zn | | Descriptor: | SULFATE ION, ZINC ION, creatinine amidohydrolase | | Authors: | Yoshimoto, T, Tanaka, N, Kanada, N, Inoue, T, Nakajima, Y, Haratake, M, Nakamura, K.T, Xu, Y, Ito, K. | | Deposit date: | 2003-01-11 | | Release date: | 2004-01-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
J.Mol.Biol., 337, 2004
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1KOL
 | | Crystal structure of formaldehyde dehydrogenase | | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SULFATE ION, ZINC ION, ... | | Authors: | Tanaka, N, Kusakabe, Y, Ito, K, Yoshimoto, T, Nakamura, K.T. | | Deposit date: | 2001-12-21 | | Release date: | 2002-12-11 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Crystal Structure of Formaldehyde Dehydrogenase from Pseudomonas putida: the Structural Origin of the Tightly Bound Cofactor in Nicotinoprotein Dehydrogenases
J.mol.biol., 324, 2002
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1ZOV
 | | Crystal Structure of Monomeric Sarcosine Oxidase from Bacillus sp. NS-129 | | Descriptor: | CHLORIDE ION, FLAVIN-ADENINE DINUCLEOTIDE, Monomeric sarcosine oxidase | | Authors: | Nagata, K, Sasaki, H, Ohtsuka, J, Hua, M, Okai, M, Kubota, K, Kamo, M, Ito, K, Ichikawa, T, Koyama, Y, Tanokura, M. | | Deposit date: | 2005-05-14 | | Release date: | 2006-05-23 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Crystal structure of monomeric sarcosine oxidase from Bacillus sp. NS-129 reveals multiple conformations at the active-site loop
PROC.JPN.ACAD.,SER.B, 81, 2005
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1X2E
 | | The crystal structure of prolyl aminopeptidase complexed with Ala-TBODA | | Descriptor: | (2S)-2-AMINO-1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)PROPAN-1-ONE, Proline iminopeptidase | | Authors: | Nakajima, Y, Ito, K, Sakata, M, Xu, Y, Matsubara, F, Hatakeyama, S, Yoshimoto, T. | | Deposit date: | 2005-04-22 | | Release date: | 2006-05-09 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens
J.Bacteriol., 188, 2006
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1X2B
 | | The crystal structure of prolyl aminopeptidase complexed with Sar-TBODA | | Descriptor: | 1-(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)-2-(METHYLAMINO)ETHANONE, Proline iminopeptidase | | Authors: | Nakajima, Y, Ito, K, Sakata, M, Xu, Y, Matsubara, F, Hatakeyama, S, Yoshimoto, T. | | Deposit date: | 2005-04-22 | | Release date: | 2006-05-09 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Unusual extra space at the active site and high activity for acetylated hydroxyproline of prolyl aminopeptidase from Serratia marcescens
J.Bacteriol., 188, 2006
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2ZTV
 | | The binary complex of D-3-hydroxybutyrate dehydrogenase with NAD+ | | Descriptor: | D(-)-3-hydroxybutyrate dehydrogenase, GLYCEROL, MAGNESIUM ION, ... | | Authors: | Nakashima, K, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2008-10-09 | | Release date: | 2009-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
J.Biochem., 145, 2009
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2ZTL
 | | Closed conformation of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ and L-3-hydroxybutyrate | | Descriptor: | (3S)-3-HYDROXYBUTANOIC ACID, D(-)-3-hydroxybutyrate dehydrogenase, GLYCEROL, ... | | Authors: | Nakashima, K, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2008-10-07 | | Release date: | 2009-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
J.Biochem., 145, 2009
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2ZTU
 | | T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ | | Descriptor: | D(-)-3-hydroxybutyrate dehydrogenase, MAGNESIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE | | Authors: | Nakashima, K, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2008-10-09 | | Release date: | 2009-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
J.Biochem., 145, 2009
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2ZTM
 | | T190S mutant of D-3-hydroxybutyrate dehydrogenase | | Descriptor: | (3S)-3-HYDROXYBUTANOIC ACID, D(-)-3-hydroxybutyrate dehydrogenase, MAGNESIUM ION, ... | | Authors: | Nakashima, K, Nakajima, Y, Ito, K, Yoshimoto, T. | | Deposit date: | 2008-10-07 | | Release date: | 2009-08-25 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
J.Biochem., 145, 2009
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3A6J
 | | E122Q mutant creatininase complexed with creatine | | Descriptor: | Creatinine amidohydrolase, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-09-02 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
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3A6D
 | | Creatininase complexed with 1-methylguanidine | | Descriptor: | 1-METHYLGUANIDINE, Creatinine amidohydrolase, MANGANESE (II) ION, ... | | Authors: | Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T. | | Deposit date: | 2009-08-31 | | Release date: | 2010-02-09 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
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