List of works - Yuichi Koga

Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog ofSulfolobus tokodaiiRNase H1

scientific article

Affinity shift of ATP upon glycerol binding to a glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1

scientific article published on 30 January 2020

Application of femtosecond laser ablation for detaching grown protein crystals from glass capillary tube

scientific article

Characteristic features of kynurenine aminotransferase allosterically regulated by (alpha)-ketoglutarate in cooperation with kynurenine

scientific article

Conformational contagion in a protein: structural properties of a chameleon sequence

scientific article

Crystal structure of N-domain of FKBP22 from Shewanella sp. SIB1: Dimer dissociation by disruption of Val-Leu knot

scientific article

Crystal structure of Tk-subtilisin folded without propeptide: requirement of propeptide for acceleration of folding

scientific article

Crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation

scientific article

Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution.

scientific article

Crystal structure of a subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis: requirement of a C-terminal beta-jelly roll domain for hyperstability

scientific article

Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form

scientific article

Crystal structure of stable protein CutA1 from psychrotrophic bacterium Shewanella sp. SIB1

scientific article

Crystal structure of unautoprocessed precursor of subtilisin from a hyperthermophilic archaeon: evidence for Ca2+-induced folding

scientific article

Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis

scientific article published on 27 January 2007

Crystallization and preliminary X-ray diffraction study of thermostable RNase HIII from Bacillus stearothermophilus

scientific article

Destabilization of psychrotrophic RNase HI in a localized fashion as revealed by mutational and X-ray crystallographic analyses

scientific article

Effect of ultrasonic irradiation on protein crystallization

Engineering of monomeric FK506-binding protein 22 with peptidyl prolyl cis-trans isomerase. Importance of a V-shaped dimeric structure for binding to protein substrate.

scientific article published on 25 June 2009

Enzymatic activity of a subtilisin homolog, Tk-SP, from Thermococcus kodakarensis in detergents and its ability to degrade the abnormal prion protein

scientific article

Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins

scientific article

Evolvability of thermophilic proteins from archaea and bacteria

scientific article published on 3 July 2013

Extracellular overproduction and preliminary crystallographic analysis of a family I.3 lipase

scientific article published on 10 February 2007

FK506-Binding protein 22 from a psychrophilic bacterium, a cold shock-inducible peptidyl prolyl isomerase with the ability to assist in protein folding

scientific article

Flavobacterium banpakuense sp. nov., isolated from leaf-and-branch compost.

scientific article

Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae.

scientific article

Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation

scientific article

Hyperthermophilic Subtilisin-Like Proteases From Thermococcus kodakarensis

Identification of the interactions critical for propeptide-catalyzed folding of Tk-subtilisin

scientific article

Identification of the substrate binding site in the N-terminal TBP-like domain of RNase H3

scientific article

Inhibition of chymotrypsin- and subtilisin-like serine proteases with Tk-serpin from hyperthermophilic archaeon Thermococcus kodakaraensis

scientific article

Insertion loop-mediated folding propagation governs efficient maturation of hyperthermophilic Tk-subtilisin at high temperatures

scientific article published on 12 December 2020

Isolation of a novel cutinase homolog with polyethylene terephthalate-degrading activity from leaf-branch compost by using a metagenomic approach.

scientific article

Laser-induced nucleation in protein crystallization: Local increase in protein concentration induced by femtosecond laser irradiation

Protein Crystal Growth Using Laser-Processed Seed Crystals

Protein core adaptability: crystal structures of the cavity-filling variants of Escherichia coli RNase HI

scientific article

Protein thermostabilization requires a fine-tuned placement of surface-charged residues

scientific article

Requirement of Ca(2+) ions for the hyperthermostability of Tk-subtilisin from Thermococcus kodakarensis

scientific article

Requirement of a unique Ca(2+)-binding loop for folding of Tk-subtilisin from a hyperthermophilic archaeon

scientific article

Requirement of left-handed glycine residue for high stability of the Tk-subtilisin propeptide as revealed by mutational and crystallographic analyses

scientific article

Role of N-terminal extension of Bacillus stearothermophilus RNase H2 and C-terminal extension of Thermotoga maritima RNase H2.

scientific article

Role of polar and nonpolar residues at the active site for PPIase activity of FKBP22 from Shewanella sp. SIB1.

scientific article

Stabilization by Fusion to the C-terminus of Hyperthermophile Sulfolobus tokodaii RNase HI: A Possibility of Protein Stabilization Tag

scientific article

Structural and thermodynamic analyses of Escherichia coli RNase HI variant with quintuple thermostabilizing mutations

scientific article

Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI

scientific article

Structure and stability of a thermostable carboxylesterase from the thermoacidophilic archaeon Sulfolobus tokodaii

scientific article

X-ray crystallographic and MD simulation studies on the mechanism of interfacial activation of a family I.3 lipase with two lids

scientific article

List of works by Yuichi Koga

Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog ofSulfolobus tokodaiiRNase H1

Affinity shift of ATP upon glycerol binding to a glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1

Application of femtosecond laser ablation for detaching grown protein crystals from glass capillary tube

Characteristic features of kynurenine aminotransferase allosterically regulated by (alpha)-ketoglutarate in cooperation with kynurenine

Conformational contagion in a protein: structural properties of a chameleon sequence

Crystal structure of N-domain of FKBP22 from Shewanella sp. SIB1: Dimer dissociation by disruption of Val-Leu knot

Crystal structure of Tk-subtilisin folded without propeptide: requirement of propeptide for acceleration of folding

Crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation

Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution.

Crystal structure of a subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis: requirement of a C-terminal beta-jelly roll domain for hyperstability

Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form

Crystal structure of stable protein CutA1 from psychrotrophic bacterium Shewanella sp. SIB1

Crystal structure of unautoprocessed precursor of subtilisin from a hyperthermophilic archaeon: evidence for Ca2+-induced folding

Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis

Crystallization and preliminary X-ray diffraction study of thermostable RNase HIII from Bacillus stearothermophilus

Destabilization of psychrotrophic RNase HI in a localized fashion as revealed by mutational and X-ray crystallographic analyses

Effect of ultrasonic irradiation on protein crystallization

Engineering of monomeric FK506-binding protein 22 with peptidyl prolyl cis-trans isomerase. Importance of a V-shaped dimeric structure for binding to protein substrate.

Enzymatic activity of a subtilisin homolog, Tk-SP, from Thermococcus kodakarensis in detergents and its ability to degrade the abnormal prion protein

Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins

Evolvability of thermophilic proteins from archaea and bacteria

Extracellular overproduction and preliminary crystallographic analysis of a family I.3 lipase

FK506-Binding protein 22 from a psychrophilic bacterium, a cold shock-inducible peptidyl prolyl isomerase with the ability to assist in protein folding

Flavobacterium banpakuense sp. nov., isolated from leaf-and-branch compost.

Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae.

Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation

Hyperthermophilic Subtilisin-Like Proteases From Thermococcus kodakarensis

Identification of the interactions critical for propeptide-catalyzed folding of Tk-subtilisin

Identification of the substrate binding site in the N-terminal TBP-like domain of RNase H3

Inhibition of chymotrypsin- and subtilisin-like serine proteases with Tk-serpin from hyperthermophilic archaeon Thermococcus kodakaraensis

Insertion loop-mediated folding propagation governs efficient maturation of hyperthermophilic Tk-subtilisin at high temperatures

Isolation of a novel cutinase homolog with polyethylene terephthalate-degrading activity from leaf-branch compost by using a metagenomic approach.

Laser-induced nucleation in protein crystallization: Local increase in protein concentration induced by femtosecond laser irradiation

Protein Crystal Growth Using Laser-Processed Seed Crystals

Protein core adaptability: crystal structures of the cavity-filling variants of Escherichia coli RNase HI

Protein thermostabilization requires a fine-tuned placement of surface-charged residues

Requirement of Ca(2+) ions for the hyperthermostability of Tk-subtilisin from Thermococcus kodakarensis

Requirement of a unique Ca(2+)-binding loop for folding of Tk-subtilisin from a hyperthermophilic archaeon

Requirement of left-handed glycine residue for high stability of the Tk-subtilisin propeptide as revealed by mutational and crystallographic analyses

Role of N-terminal extension of Bacillus stearothermophilus RNase H2 and C-terminal extension of Thermotoga maritima RNase H2.

Role of polar and nonpolar residues at the active site for PPIase activity of FKBP22 from Shewanella sp. SIB1.

Stabilization by Fusion to the C-terminus of Hyperthermophile Sulfolobus tokodaii RNase HI: A Possibility of Protein Stabilization Tag

Structural and thermodynamic analyses of Escherichia coli RNase HI variant with quintuple thermostabilizing mutations

Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI

Structure and stability of a thermostable carboxylesterase from the thermoacidophilic archaeon Sulfolobus tokodaii

X-ray crystallographic and MD simulation studies on the mechanism of interfacial activation of a family I.3 lipase with two lids