3LQB
 
 | | Crystal structure of the hatching enzyme ZHE1 from the zebrafish Danio rerio | | Descriptor: | 1,2-ETHANEDIOL, LOC792177 protein, SULFATE ION, ... | | Authors: | Tanokura, M, Okada, A, Nagata, K, Yasumasu, S, Ohtsuka, J, Iuchi, I. | | Deposit date: | 2010-02-08 | | Release date: | 2010-09-08 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Crystal structure of zebrafish hatching enzyme 1 from the zebrafish Danio rerio
J.Mol.Biol., 402, 2010
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2E3U
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3AEV
 | | Crystal structure of a/eIF2alpha-aDim2p-rRNA complex from Pyrococcus horikoshii OT3 | | Descriptor: | Putative uncharacterized protein PH1566, RNA (5'-R(*GP*GP*AP*UP*CP*AP*CP*CP*UP*CP*C)-3'), Translation initiation factor 2 subunit alpha | | Authors: | Tanokura, M, Jia, M.Z, Nagata, K. | | Deposit date: | 2010-02-10 | | Release date: | 2010-04-21 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | An archaeal Dim2-like protein, aDim2p, forms a ternary complex with a/eIF2 alpha and the 3' end fragment of 16S rRNA
J.Mol.Biol., 398, 2010
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1VFR
 | | THE MAJOR NAD(P)H:FMN OXIDOREDUCTASE FROM VIBRIO FISCHERI | | Descriptor: | FLAVIN MONONUCLEOTIDE, NAD(P)H:FMN OXIDOREDUCTASE | | Authors: | Koike, H, Sasaki, H, Kobori, T, Zenno, S, Saigo, K, Murphy, M.E.P, Adman, E.T, Tanokura, M. | | Deposit date: | 1998-01-09 | | Release date: | 1999-02-16 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | 1.8 A crystal structure of the major NAD(P)H:FMN oxidoreductase of a bioluminescent bacterium, Vibrio fischeri: overall structure, cofactor and substrate-analog binding, and comparison with related flavoproteins.
J.Mol.Biol., 280, 1998
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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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2RR7
 | | Microtubule Binding Domain of DYNEIN-C | | Descriptor: | Dynein heavy chain 9 | | Authors: | Kato, Y, Yagi, T, Ohki, S, Burgess, S, Honda, S, Kamiya, R, Tanokura, M. | | Deposit date: | 2010-06-04 | | Release date: | 2011-06-08 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structure of the microtubule-binding domain of flagellar dynein
Structure, 22, 2014
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5IFF
 | | Crystal structure of R.PabI-nonspecific DNA complex | | Descriptor: | DNA (5'-D(*GP*CP*AP*CP*TP*AP*GP*TP*TP*CP*GP*AP*AP*CP*TP*AP*GP*TP*GP*C)-3'), Uncharacterized protein | | Authors: | Wang, D, Miyazono, K, Tanokura, M. | | Deposit date: | 2016-02-26 | | Release date: | 2016-11-23 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.
Sci Rep, 6, 2016
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6L2N
 | | Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-3bp-GTAC) complex | | Descriptor: | DNA (5'-D(*TP*CP*AP*GP*CP*AP*GP*TP*AP*CP*TP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*GP*A)-3'), RE_R_Pab1 domain-containing protein | | Authors: | Miyazono, K, Wang, D, Ito, T, Tanokura, M. | | Deposit date: | 2019-10-05 | | Release date: | 2020-03-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.
Nucleic Acids Res., 48, 2020
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6L2O
 | | Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(GTAC-5bp-GTAC) complex | | Descriptor: | DNA (5'-D(*CP*A*GP*CP*AP*GP*TP*AP*CP*TP*TP*AP*AP*AP*GP*TP*AP*CP*TP*GP*CP*TP*G)-3'), RE_R_Pab1 domain-containing protein | | Authors: | Miyazono, K, Wang, D, Ito, T, Tanokura, M. | | Deposit date: | 2019-10-05 | | Release date: | 2020-03-18 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.
Nucleic Acids Res., 48, 2020
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1F5V
 | | STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF A FLAVOPROTEIN FROM ESCHERICHIA COLI THAT REDUCES NITROCOMPOUNDS. ALTERATION OF PYRIDINE NUCLEOTIDE BINDING BY A SINGLE AMINO ACID SUBSTITUTION | | Descriptor: | FLAVIN MONONUCLEOTIDE, OXYGEN-INSENSITIVE NADPH NITROREDUCTASE | | Authors: | Kobori, T, Sasaki, H, Lee, W.C, Zenno, S, Saigo, K, Murphy, M.E.P, Tanokura, M. | | Deposit date: | 2000-06-17 | | Release date: | 2001-02-14 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structure and site-directed mutagenesis of a flavoprotein from Escherichia coli that reduces nitrocompounds: alteration of pyridine nucleotide binding by a single amino acid substitution.
J.Biol.Chem., 276, 2001
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6AGZ
 | | Crystal structure of Old Yellow Enzyme from Pichia sp. AKU4542 | | Descriptor: | FLAVIN MONONUCLEOTIDE, Old Yellow Enzyme | | Authors: | Horita, S, Kataoka, M, Kitamura, N, Nakagawa, T, Miyakawa, T, Ohtsuka, J, Nagata, K, Shimizu, S, Tanokura, M. | | Deposit date: | 2018-08-15 | | Release date: | 2019-06-26 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds.
Biosci.Biotechnol.Biochem., 83, 2019
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3W20
 | | Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD | | Descriptor: | Putative uncharacterized protein, ZINC ION | | Authors: | Qin, H.M, Miyakawa, T, Jia, M.Z, Nakamura, A, Ohtsuka, J, Xue, Y.L, Kawashima, T, Kasahara, T, Hibi, M, Ogawa, J, Tanokura, M. | | Deposit date: | 2012-11-26 | | Release date: | 2013-07-17 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD
Plos One, 8, 2013
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3W21
 | | Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD | | Descriptor: | 2-OXOGLUTARIC ACID, Putative uncharacterized protein, ZINC ION | | Authors: | Qin, H.M, Miyakawa, T, Jia, M.Z, Nakamura, A, Ohtsuka, J, Xue, Y.L, Kawashima, T, Kasahara, T, Hibi, M, Ogawa, J, Tanokura, M. | | Deposit date: | 2012-11-26 | | Release date: | 2013-07-17 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD
Plos One, 8, 2013
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5TLC
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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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2YQY
 | | Crystal structure of TT2238, a four-helix bundle protein | | Descriptor: | Hypothetical protein TTHA0303 | | Authors: | Nagata, K, Ohtsuka, J, Iino, H, Ebihara, A, Yokoyama, S, Kuramitsu, S, Tanokura, M. | | Deposit date: | 2007-03-31 | | Release date: | 2008-03-04 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 A
Proteins, 70, 2008
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3VXG
 | | Crystal structure of conjugated polyketone reductase C2 from Candida Parapsilosis | | Descriptor: | Conjugated polyketone reductase C2 | | Authors: | Qin, H.-M, Yamamura, A, Miyakawa, T, Maruoka, S, Ohtsuka, J, Nagata, K, Kataoka, M, Shimizu, S, Tanokura, M. | | Deposit date: | 2012-09-13 | | Release date: | 2013-08-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.7 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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4O0L
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3VVU
 | | Crystal structure of reconstructed bacterial ancestral NDK, Bac1 | | Descriptor: | Nucleoside diphosphate kinase | | Authors: | Nemoto, N, Miyazono, K, Kimura, M, Yokobori, S, Akanuma, S, Tanokura, M, Yamagishi, A. | | Deposit date: | 2012-07-27 | | Release date: | 2013-06-19 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Experimental evidence for the thermophilicity of ancestral life
Proc.Natl.Acad.Sci.USA, 110, 2013
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3VVT
 | | Crystal structure of reconstructed archaeal ancestral NDK, Arc1 | | Descriptor: | Nucleoside diphosphate kinase | | Authors: | Nemoto, N, Miyazono, K, Kimura, M, Yokobori, S, Akanuma, S, Tanokura, M, Yamagishi, A. | | Deposit date: | 2012-07-27 | | Release date: | 2013-06-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Experimental evidence for the thermophilicity of ancestral life
Proc.Natl.Acad.Sci.USA, 110, 2013
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3EOQ
 | | The crystal structure of putative zinc protease beta-subunit from Thermus thermophilus HB8 | | Descriptor: | Putative zinc protease | | Authors: | Ohtsuka, J, Ichihara, Y, Ebihara, A, Yokoyama, S, Kuramitsu, S, Nagata, K, Tanokura, M. | | Deposit date: | 2008-09-29 | | Release date: | 2009-03-17 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.29 Å) | | Cite: | Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the beta subunit of mitochondrial processing peptidase.
Proteins, 2009
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3VS9
 | | Crystal structure of type III PKS ArsC mutant | | Descriptor: | SODIUM ION, TETRAETHYLENE GLYCOL, Type III polyketide synthase | | Authors: | Satou, R, Miyanaga, A, Ozawa, H, Funa, N, Miyazono, K, Tanokura, M, Ohnishi, Y, Horinouchi, S. | | Deposit date: | 2012-04-23 | | Release date: | 2013-04-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Structural basis for cyclization specificity of two Azotobacter type III polyketide synthases: a single amino acid substitution reverses their cyclization specificity
J.Biol.Chem., 288, 2013
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3VGK
 | | Crystal structure of a ROK family glucokinase from Streptomyces griseus | | Descriptor: | Glucokinase, SULFATE ION, ZINC ION | | Authors: | Miyazono, K, Tabei, N, Morita, S, Ohnishi, Y, Horinouchi, S, Tanokura, M. | | Deposit date: | 2011-08-15 | | Release date: | 2011-12-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.25 Å) | | Cite: | Substrate recognition mechanism and substrate-dependent conformational changes of an ROK family glucokinase from Streptomyces griseus
J.Bacteriol., 194, 2012
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3VS8
 | | Crystal structure of type III PKS ArsC | | Descriptor: | SODIUM ION, Type III polyketide synthase | | Authors: | Satou, R, Miyanaga, A, Ozawa, H, Funa, N, Miyazono, K, Tanokura, M, Ohnishi, Y, Horinouchi, S. | | Deposit date: | 2012-04-23 | | Release date: | 2013-04-24 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.76 Å) | | Cite: | Structural basis for cyclization specificity of two Azotobacter type III polyketide synthases: a single amino acid substitution reverses their cyclization specificity
J.Biol.Chem., 288, 2013
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6M64
 | | Crystal structure of SMAD2 in complex with CBP | | Descriptor: | CBP, Mothers against decapentaplegic homolog 2 | | Authors: | Miyazono, K, Ito, T, Wada, H, Tanokura, M. | | Deposit date: | 2020-03-13 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural basis for transcriptional coactivator recognition by SMAD2 in TGF-beta signaling.
Sci.Signal., 13, 2020
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