List of works - Koji Nagata

1H, 13C and 15N assignments of the tandem WW domains of human MAGI-1/BAP-1.

scientific article published in August 2004

1H, 13C, 15N resonance assignments of the cytokine LECT2.

scientific article published in August 2004

A class-A GPCR solubilized under high hydrostatic pressure retains its ligand binding ability.

scientific article published on 21 June 2016

An engineered old yellow enzyme that enables efficient synthesis of (4R,6R)-Actinol in a one-pot reduction system

scientific article

Apolipoprotein E binds to and reduces serum levels of DNA-mimicking, pyrrolated proteins

scientific article published on 05 June 2019

Assignment of 1H, 13C and 15N resonances of FKBP. from Methanococcus thermolithotrophicus

scientific article published on 01 June 2000

Biological actions of green tea catechins on cardiac troponin C.

scientific article

Bombyxin secretion in the adult silkmoth Bombyx mori: sex-specificity and its correlation with metabolism

scientific article published on 01 October 1999

Bombyxin-II and its disulfide bond isomers: synthesis and activity

scientific article published on July 1, 1992

Characterization of native and recombinant peptidyl prolyl cis-trans isomerases derived from Methanococcus thermolithotrophicus based on cDNA sequence

scientific article published on 01 May 2000

Common mechanism of ligand recognition by group II/III WW domains: redefining their functional classification.

scientific article

Comparison of physiological functions of antagonistic insulin-like peptides, INS-23 and INS-18, in Caenorhabditis elegans.

scientific article

Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity

scientific article

Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless

scientific article

Coordination structures of Ca2+ and Mg2+ in Akazara scallop troponin C in solution. FTIR spectroscopy of side-chain COO- groups

scientific article published on 01 December 2001

Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 A

scientific article

Crystal structure of TTHA1429, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8

scientific article

Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase

scientific article

Crystal structure of a crustacean hyperglycemic hormone (CHH) precursor suggests structural variety in the C-terminal regions of CHH superfamily members

scientific article

Crystal structure of conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 complexed with NADPH

scientific article

Crystal structure of the YjgF/YER057c/UK114 family protein from the hyperthermophilic archaeon Sulfolobus tokodaii strain 7

scientific article published on 01 February 2006

Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea Sulfolobus tokodaii strain7

scientific article

Crystal structure of zebrafish hatching enzyme 1 from the zebrafish Danio rerio

scientific article

Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound

scientific article published on 01 April 2006

Crystallization and preliminary X-ray analysis of 5-keto-D-gluconate reductase from Gluconobacter suboxydans IFO12528 complexed with 5-keto-D-gluconate and NADPH.

scientific article published on 27 November 2010

Crystallization and preliminary X-ray analysis of a putative sensor histidine kinase domain: the C-terminal domain of HksP4 from Aquifex aeolicus VF5.

scientific article published on 30 June 2011

Crystallization and preliminary X-ray analysis of carboxypeptidase 1 from Thermus thermophilus.

scientific article published on 21 July 2004

Crystallization and preliminary X-ray analysis of the C-terminal RNase III domain of human Dicer.

scientific article

Crystallization and preliminary X-ray analysis of the Ca2+-bound C-terminal lobe of troponin C in complex with a troponin I-derived peptide fragment from Akazara scallop.

scientific article published on 31 May 2007

Crystallization and preliminary X-ray analysis of the NADPH-dependent 3-quinuclidinone reductase from Rhodotorula rubra.

scientific article published on 23 May 2009

Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6.

scientific article published on 31 July 2012

Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building.

scientific article published on 20 December 2001

Drastic Ca2+ sensitization of myofilament associated with a small structural change in troponin I in inherited restrictive cardiomyopathy.

scientific article

Establishment of Sf9 Transformants Constitutively Expressing PBAN Receptor Variants: Application to Functional Evaluation.

scientific article

Expression, purification, crystallization and X-ray analysis of 3-quinuclidinone reductase from Agrobacterium tumefaciens.

scientific article published on 29 September 2012

Expression, purification, crystallization and preliminary X-ray analysis of 4-hydroxy-3-methyl-2-keto-pentanoate aldolase (asHPAL) from Arthrobacter simplex strain AKU 626

scientific article published on 31 July 2012

Expression, purification, crystallization and preliminary X-ray analysis of conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708.

scientific article published on 30 October 2009

Functional characterisation of two ferric-ion coordination modes of TtFbpA, the periplasmic subunit of an ABC-type iron transporter from Thermus thermophilus HB8

scientific article published on 01 December 2019

G-Protein Coupled Receptor Protein Synthesis on a Lipid Bilayer Using a Reconstituted Cell-Free Protein Synthesis System

scientific article published on 02 November 2018

Heme protein identified from scaly-foot gastropod can synthesize pyrite (FeS2) nanoparticles

scientific article published in 2023

High pressure refolding, purification, and crystallization of flavin reductase from Sulfolobus tokodaii strain 7.

scientific article published on 19 June 2012

Human CTP:phosphoethanolamine cytidylyltransferase: enzymatic properties and unequal catalytic roles of CTP-binding motifs in two cytidylyltransferase domains.

scientific article

Identification of functionally important residues of the silkmoth pheromone biosynthesis-activating neuropeptide receptor, an insect ortholog of the vertebrate neuromedin U receptor.

scientific article

Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase.

scientific article published in February 2017

Isolation, cDNA Cloning, and Structure-based Functional Characterization of Oryctin, a Hemolymph Protein from the Coconut Rhinoceros Beetle, Oryctes rhinoceros, as a Novel Serine Protease Inhibitor

scientific article

Mechanism of self/nonself-discrimination in Brassica self-incompatibility

scientific article published on 01 October 2020

Molecular Mechanism of Distinct Salt-Dependent Enzyme Activity of Two Halophilic Nucleoside Diphosphate Kinases

scientific article

NMR structural study of troponin C C-terminal domain complexed with troponin I fragment from Akazara scallop.

scientific article published in January 2003

Novel protein fold discovered in the PabI family of restriction enzymes

scientific article published in 2007

Oxidative deamination of lysine residues by polyphenols generates an equilibrium of aldehyde and 2-piperidinol products

scientific article published on 31 July 2021

Preliminary X-ray crystallographic analysis of thermolysin in the presence of 4 M NaCl

scientific article published on 26 May 2005

Purification and gene cloning of Fundulus heteroclitus hatching enzyme. A hatching enzyme system composed of high choriolytic enzyme and low choriolytic enzyme is conserved between two different teleosts, Fundulus heteroclitus and medaka Oryzias lat

scientific article published in September 2005

Purification, crystallization and preliminary X-ray analysis of L-sorbose reductase from Gluconobacter frateurii complexed with L-sorbose or NADPH

scientific article published on 22 May 2009

Purification, crystallization and preliminary X-ray analysis of the DNA-binding domain of AdpA, the central transcription factor in the A-factor regulatory cascade in the filamentous bacterium Streptomyces griseus, in complex with a duplex DNA

scientific article published on 31 July 2012

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding

scientific article

Re-Evaluation of the PBAN Receptor Molecule: Characterization of PBANR Variants Expressed in the Pheromone Glands of Moths.

scientific article

Reversible and irreversible coiled coils in the stalk domain of ncd motor protein.

scientific article published on 27 July 2007

Siamycin attenuates fsr quorum sensing mediated by a gelatinase biosynthesis-activating pheromone in Enterococcus faecalis.

scientific article published on 27 October 2006

Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III

scientific article published on 01 April 2006

Solution structure of a short-chain insecticidal toxin LaIT1 from the venom of scorpion Liocheles australasiae

scientific article

Solution structure of the SH2 domain of Grb2/Ash complexed with EGF receptor-derived phosphotyrosine-containing peptide

scientific article published on 01 June 1999

Spectroscopic and ITC study of the conformational change upon Ca2+-binding in TnC C-lobe and TnI peptide complex from Akazara scallop striated muscle

scientific article published on 03 December 2007

Structural basis for high substrate-binding affinity and enantioselectivity of 3-quinuclidinone reductase AtQR

scientific article published on 15 March 2014

Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds

scientific article published on 16 November 2018

Structural basis of stereospecific reduction by quinuclidinone reductase

scientific article

Structure of TTHA1623, a novel metallo-β-lactamase superfamily protein fromThermus thermophilusHB8

scientific article

Structure of calcium-bound human S100A13 at pH 7.5 at 1.8 Å resolution

scientific article

Structure-activity relationship of gelatinase biosynthesis-activating pheromone of Enterococcus faecalis

scientific article

Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.

scientific article published on 07 March 2010

Synthesis of bombyxin-IV, an insulin superfamily peptide from the silkworm, Bombyx mori, by stepwise and selective formation of three disulfide bridges

scientific article published on February 1, 1992

The structure of brazzein, a sweet-tasting protein from the wild African plant Pentadiplandra brazzeana

scientific article

The structure of mAG, a monomeric mutant of the green fluorescent protein Azami-Green, reveals the structural basis of its stable green emission

scientific article

Three-dimensional solution structure of an archaeal FKBP with a dual function of peptidyl prolyl cis-trans isomerase and chaperone-like activities

scientific article (publication date: 16 May 2003)

Three-dimensional solution structure of oryzacystatin-I, a cysteine proteinase inhibitor of the rice, Oryza sativa L. japonica

scientific article

Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery.

scientific article published on 6 January 2017

List of works by Koji Nagata

1H, 13C and 15N assignments of the tandem WW domains of human MAGI-1/BAP-1.

1H, 13C, 15N resonance assignments of the cytokine LECT2.

A class-A GPCR solubilized under high hydrostatic pressure retains its ligand binding ability.

An engineered old yellow enzyme that enables efficient synthesis of (4R,6R)-Actinol in a one-pot reduction system

Apolipoprotein E binds to and reduces serum levels of DNA-mimicking, pyrrolated proteins

Assignment of 1H, 13C and 15N resonances of FKBP. from Methanococcus thermolithotrophicus

Biological actions of green tea catechins on cardiac troponin C.

Bombyxin secretion in the adult silkmoth Bombyx mori: sex-specificity and its correlation with metabolism

Bombyxin-II and its disulfide bond isomers: synthesis and activity

Characterization of native and recombinant peptidyl prolyl cis-trans isomerases derived from Methanococcus thermolithotrophicus based on cDNA sequence

Common mechanism of ligand recognition by group II/III WW domains: redefining their functional classification.

Comparison of physiological functions of antagonistic insulin-like peptides, INS-23 and INS-18, in Caenorhabditis elegans.

Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity

Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless

Coordination structures of Ca2+ and Mg2+ in Akazara scallop troponin C in solution. FTIR spectroscopy of side-chain COO- groups

Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 A

Crystal structure of TTHA1429, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8

Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase

Crystal structure of a crustacean hyperglycemic hormone (CHH) precursor suggests structural variety in the C-terminal regions of CHH superfamily members

Crystal structure of conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 complexed with NADPH

Crystal structure of the YjgF/YER057c/UK114 family protein from the hyperthermophilic archaeon Sulfolobus tokodaii strain 7

Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea Sulfolobus tokodaii strain7

Crystal structure of zebrafish hatching enzyme 1 from the zebrafish Danio rerio

Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states: NAD(P)(+)(-)free, NAD(+)(-)bound, and NADP(+)(-)bound

Crystallization and preliminary X-ray analysis of 5-keto-D-gluconate reductase from Gluconobacter suboxydans IFO12528 complexed with 5-keto-D-gluconate and NADPH.

Crystallization and preliminary X-ray analysis of a putative sensor histidine kinase domain: the C-terminal domain of HksP4 from Aquifex aeolicus VF5.

Crystallization and preliminary X-ray analysis of carboxypeptidase 1 from Thermus thermophilus.

Crystallization and preliminary X-ray analysis of the C-terminal RNase III domain of human Dicer.

Crystallization and preliminary X-ray analysis of the Ca2+-bound C-terminal lobe of troponin C in complex with a troponin I-derived peptide fragment from Akazara scallop.

Crystallization and preliminary X-ray analysis of the NADPH-dependent 3-quinuclidinone reductase from Rhodotorula rubra.

Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6.

Determinants of ligand specificity in groups I and IV WW domains as studied by surface plasmon resonance and model building.

Drastic Ca2+ sensitization of myofilament associated with a small structural change in troponin I in inherited restrictive cardiomyopathy.

Establishment of Sf9 Transformants Constitutively Expressing PBAN Receptor Variants: Application to Functional Evaluation.

Expression, purification, crystallization and X-ray analysis of 3-quinuclidinone reductase from Agrobacterium tumefaciens.

Expression, purification, crystallization and preliminary X-ray analysis of 4-hydroxy-3-methyl-2-keto-pentanoate aldolase (asHPAL) from Arthrobacter simplex strain AKU 626

Expression, purification, crystallization and preliminary X-ray analysis of conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708.

Functional characterisation of two ferric-ion coordination modes of TtFbpA, the periplasmic subunit of an ABC-type iron transporter from Thermus thermophilus HB8

G-Protein Coupled Receptor Protein Synthesis on a Lipid Bilayer Using a Reconstituted Cell-Free Protein Synthesis System

Heme protein identified from scaly-foot gastropod can synthesize pyrite (FeS2) nanoparticles

High pressure refolding, purification, and crystallization of flavin reductase from Sulfolobus tokodaii strain 7.

Human CTP:phosphoethanolamine cytidylyltransferase: enzymatic properties and unequal catalytic roles of CTP-binding motifs in two cytidylyltransferase domains.

Identification of functionally important residues of the silkmoth pheromone biosynthesis-activating neuropeptide receptor, an insect ortholog of the vertebrate neuromedin U receptor.

Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase.

Isolation, cDNA Cloning, and Structure-based Functional Characterization of Oryctin, a Hemolymph Protein from the Coconut Rhinoceros Beetle, Oryctes rhinoceros, as a Novel Serine Protease Inhibitor

Mechanism of self/nonself-discrimination in Brassica self-incompatibility

Molecular Mechanism of Distinct Salt-Dependent Enzyme Activity of Two Halophilic Nucleoside Diphosphate Kinases

NMR structural study of troponin C C-terminal domain complexed with troponin I fragment from Akazara scallop.

Novel protein fold discovered in the PabI family of restriction enzymes

Oxidative deamination of lysine residues by polyphenols generates an equilibrium of aldehyde and 2-piperidinol products

Preliminary X-ray crystallographic analysis of thermolysin in the presence of 4 M NaCl

Purification and gene cloning of Fundulus heteroclitus hatching enzyme. A hatching enzyme system composed of high choriolytic enzyme and low choriolytic enzyme is conserved between two different teleosts, Fundulus heteroclitus and medaka Oryzias lat

Purification, crystallization and preliminary X-ray analysis of L-sorbose reductase from Gluconobacter frateurii complexed with L-sorbose or NADPH

Purification, crystallization and preliminary X-ray analysis of the DNA-binding domain of AdpA, the central transcription factor in the A-factor regulatory cascade in the filamentous bacterium Streptomyces griseus, in complex with a duplex DNA

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding

Re-Evaluation of the PBAN Receptor Molecule: Characterization of PBANR Variants Expressed in the Pheromone Glands of Moths.

Reversible and irreversible coiled coils in the stalk domain of ncd motor protein.

Siamycin attenuates fsr quorum sensing mediated by a gelatinase biosynthesis-activating pheromone in Enterococcus faecalis.

Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III

Solution structure of a short-chain insecticidal toxin LaIT1 from the venom of scorpion Liocheles australasiae

Solution structure of the SH2 domain of Grb2/Ash complexed with EGF receptor-derived phosphotyrosine-containing peptide

Spectroscopic and ITC study of the conformational change upon Ca2+-binding in TnC C-lobe and TnI peptide complex from Akazara scallop striated muscle

Structural basis for high substrate-binding affinity and enantioselectivity of 3-quinuclidinone reductase AtQR

Structural basis of different substrate preferences of two old yellow enzymes from yeasts in the asymmetric reduction of enone compounds

Structural basis of stereospecific reduction by quinuclidinone reductase

Structure of TTHA1623, a novel metallo-β-lactamase superfamily protein fromThermus thermophilusHB8

Structure of calcium-bound human S100A13 at pH 7.5 at 1.8 Å resolution

Structure-activity relationship of gelatinase biosynthesis-activating pheromone of Enterococcus faecalis

Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.

Synthesis of bombyxin-IV, an insulin superfamily peptide from the silkworm, Bombyx mori, by stepwise and selective formation of three disulfide bridges

The structure of brazzein, a sweet-tasting protein from the wild African plant Pentadiplandra brazzeana

The structure of mAG, a monomeric mutant of the green fluorescent protein Azami-Green, reveals the structural basis of its stable green emission

Three-dimensional solution structure of an archaeal FKBP with a dual function of peptidyl prolyl cis-trans isomerase and chaperone-like activities

Three-dimensional solution structure of oryzacystatin-I, a cysteine proteinase inhibitor of the rice, Oryza sativa L. japonica

Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery.