K. Yokoyama

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Crystal structure of A3B3 complex of V-ATPase from Thermus thermophilus

Masasuke Yoshida, S. Yokoyama, M. Maher, 2009, The EMBO journal.

Crystal structure of the native chaperonin complex from Thermus thermophilus revealed unexpected asymmetry at the cis-cavity.

Hideki Taguchi, So Iwata, Masasuke Yoshida, 2004, Structure.

Radical-Mediated Carbon Skeleton Formation in Cofactor and Natural Product Biosynthesis

K. Yokoyama, 2019 .

C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products.

K. Yokoyama, Edward A. Lilla, 2018, Natural product reports.

Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin.

K. Yokoyama, T. Eguchi, F. Kudo, 2007, Journal of the American Chemical Society.

Different roles of proteolipids and 70‐kDa subunits of V‐ATPase in growth and death of cultured human cells

K. Yokoyama, H. Zhan, H. Otani, 2003, Genes to cells : devoted to molecular & cellular mechanisms.

The TF1-ATPase and ATPase activities of assembled α3β3γ, α3β3γδ, and α3β3γε complexes are stimulated by low and inhibited by high concentrations of rhodamine 6G whereas the dye only inhibits the α3β3, and α3β3δ complexes

Masasuke Yoshida, Y. Kagawa, K. Yokoyama, 1993, Journal of Bioenergetics and Biomembranes.

Glutamate 350 Plays an Essential Role in Conformational Gating of Long-Range Radical Transport in Escherichia coli Class Ia Ribonucleotide Reductase.

K. Yokoyama, D. Nocera, J. Stubbe, 2017, Biochemistry.

Structure of a central stalk subunit F of prokaryotic V‐type ATPase/synthase from Thermus thermophilus

Masasuke Yoshida, R. Iino, E. Carpenter, 2005, The EMBO journal.

The mechanical inhibition of the isolated Vo from V-ATPase for proton conductance

K. Namba, K. Yokoyama, K. Mitsuoka, 2020, bioRxiv.

The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by EPR and ENDOR Spectroscopies.

A. Byer, K. Yokoyama, B. Hoffman, 2019, Journal of the American Chemical Society.

Gene cloning and overexpression of a geranylgeranyl diphosphate synthase of an extremely thermophilic bacterium, Thermus thermophilus.

K. Yokoyama, T. Nishino, C. Ohto, 1999, Bioscience, biotechnology, and biochemistry.

The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria.

K. Yokoyama, S. Leimkühler, 2015, Biochimica et biophysica acta.

Identification of a cyclic nucleotide as a cryptic intermediate in molybdenum cofactor biosynthesis.

K. Yokoyama, A. Ribeiro, B. Hover, 2013, Journal of the American Chemical Society.

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

Masasuke Yoshida, J. Barber, M. Iwata, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Cryo-EM structure of the native GroEL-GroES complex from thermus thermophilus encapsulating substrate inside the cavity.

H. Taguchi, K. Yokoyama, K. Mitsuoka, 2009, Structure.

Mechanism of dimer formation of the 90-kDa heat-shock protein.

T. Takagi, K. Yokoyama, T. Nemoto, 1995, European journal of biochemistry.

N-acetylmannosaminyl(1----4)N-acetylglucosamine, a linkage unit between glycerol teichoic acid and peptidoglycan in cell walls of several Bacillus strains

K. Yokoyama, Y. Araki, S. Kaya, 1984, Journal of bacteriology.

Mechanism of inhibition of the V-type molecular motor by tributyltin chloride.

Masasuke Yoshida, K. Yokoyama, K. Shimabukuro, 2009, Biophysical journal.

4-Aminobutyraldehyde and 4-guanidinobutyraldehyde dehydrogenases for arginine degradation in Pseudomonas putida

K. Yokoyama, K. Koike, T. Yorifuji, 1986 .

MRT letter: Expression of ATP sensor protein in Caenorhabditis elegans

S. Mitani, K. Yokoyama, H. Noji, 2012, Microscopy research and technique.

Stereochemical recognition of doubly functional aminotransferase in 2-deoxystreptamine biosynthesis.

K. Yokoyama, T. Eguchi, K. Kakinuma, 2005, Journal of the American Chemical Society.

Enfumafungin synthase represents a novel lineage of fungal triterpene cyclases

K. Yokoyama, R. Cox, E. Kuhnert, 2018, Environmental microbiology.

A novel form of rhodopsin kinase from chicken retina and pineal gland 1

M. E. Whitten, M. Gelb, K. Palczewski, 1999, FEBS letters.

Accumulation of an unprecedented 5′-deoxyadenos-4′-yl radical unmasks the kinetics of the radical-mediated C-C bond formation step in MoaA catalysis

L. Scott, Weitao Yang, K. Yokoyama, 2020, bioRxiv.

V-Type H+-ATPase/Synthase from a Thermophilic Eubacterium, Thermus Thermophilus

H. Taguchi, K. Yokoyama, M. Yoshida, 2000, The Journal of Biological Chemistry.

Conserved Mechanism of 2'-Phosphorylation-Aided Amide Ligation in Peptidyl Nucleoside Biosynthesis.

K. Yokoyama, Anyarat Thanapipatsiri, Matthew M. Draelos, 2021, Biochemistry.

Structures of multisubunit membrane complexes with the CRYO ARM 200

K. Namba, K. Yokoyama, Takayuki Kato, 2022, Microscopy.

Two-dimensional crystallization and analysis of projection images of intact Thermus thermophilus V-ATPase.

Masasuke Yoshida, K. Tani, Y. Fujiyoshi, 2006, Journal of structural biology.

The F Subunit of Thermus thermophilus V1-ATPase Promotes ATPase Activity but Is Not Necessary for Rotation*

Masasuke Yoshida, K. Yokoyama, H. Imamura, 2004, Journal of Biological Chemistry.

Single site hydrolysis of 2',3'-O-(2,4,6-trinitrophenyl)-ATP by the F1-ATPase from thermophilic bacterium PS3 is accelerated by the chase-addition of excess ATP.

E. Muneyuki, K. Yokoyama, M. Yoshida, 1992, The Journal of biological chemistry.

Electron microscopy of the reconstituted complexes of the F1‐ATPase with various subunit constitution revealed the location of the γ subunit in the central cavity of the molecule

Masasuke Yoshida, K. Yokoyama, M. Yoshida, 1990, FEBS letters.

Carbon extension in peptidylnucleoside biosynthesis by radical-SAM enzymes

K. Yokoyama, Edward A. Lilla, 2016, Nature chemical biology.

Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5'-diphosphate in the presence or absence of reductant.

R. Griffin, K. Yokoyama, J. Stubbe, 2009, Biochemistry.

Mechanical Modulation of ATP-binding Affinity of V1-ATPase*

K. Yokoyama, H. Noji, Masahiro Nakano, 2012, The Journal of Biological Chemistry.

Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase

F. Asturias, K. Yokoyama, E. Brignole, 2011, Proceedings of the National Academy of Sciences.

Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis

L. Scott, A. Byer, K. Yokoyama, 2018, Journal of the American Chemical Society.

Structure and functions of linkage unit intermediates in the biosynthesis of ribitol teichoic acids in Staphylococcus aureus H and Bacillus subtilis W23.

K. Yokoyama, Y. Araki, E. Ito, 1986, European journal of biochemistry.

Lessons From the Studies of a CC Bond Forming Radical SAM Enzyme in Molybdenum Cofactor Biosynthesis.

K. Yokoyama, Haoran Pang, 2018, Methods in enzymology.

Radical Breakthroughs in Natural Product and Cofactor Biosynthesis.

K. Yokoyama, 2017, Biochemistry.

C-Terminal glycine-gated radical initiation by GTP 3',8-cyclase in the molybdenum cofactor biosynthesis.

K. Yokoyama, B. Hover, 2015, Journal of the American Chemical Society.

Structural transition of the ground-state structure to steady-state structures by sequential binding of ATP to V/A-ATPase

K. Yokoyama, K. Mitsuoka, A. Nakanishi, 2022, bioRxiv.

Quantitative Characterization of the Amount and Length of (1,3)-β-d-glucan for Functional and Mechanistic Analysis of Fungal (1,3)-β-d-glucan Synthase.

K. Yokoyama, Anna Loksztejn, Abhishek Chhetri, 2021, Bio-protocol.

Isolation of prokaryotic V0V1-ATPase from a thermophilic eubacterium Thermus thermophilus.

K. Yokoyama, M. Yoshida, N. Ishii, 1994, The Journal of biological chemistry.

Structure and glycosylation of lipoteichoic acids in Bacillus strains

K. Yokoyama, K. Yokoyama, E. Ito, 1989, Journal of bacteriology.

Mechanistic Investigation of cPMP Synthase in Molybdenum Cofactor Biosynthesis Using an Uncleavable Substrate Analogue.

K. Yokoyama, Edward A. Lilla, B. Hover, 2015, Biochemistry.

Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis

K. Yokoyama, M. Schumacher, B. Hover, 2015, Proceedings of the National Academy of Sciences.

The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by EPR and ENDOR Spectroscopies.

A. Byer, K. Yokoyama, B. Hoffman, 2019, Journal of the American Chemical Society.

Biosynthesis and Mechanism of Action of Antifungal Peptidyl Nucleoside Natural Products

K. Yokoyama, Matthew M Draelos, Matthew M. Draelos, 2019 .

Mechanism of Reduction of an Aminyl Radical Intermediate in the Radical SAM GTP 3',8-Cyclase MoaA.

S. Elliott, Weitao Yang, K. Yokoyama, 2021, Journal of the American Chemical Society.

Mechanism of rate acceleration of radical C-C bond formation reaction by a radical SAM GTP 3',8-cyclase.

L. Scott, Weitao Yang, K. Yokoyama, 2020, Journal of the American Chemical Society.

Prodigiosins uncouple mitochondrial and bacterial F-ATPases: evidence for their H+/Cl- symport activity.

K. Yokoyama, T. Kataoka, K. Nagai, 1998, Journal of biochemistry.

Molecular mechanism of energy conservation in polysulfide respiration

P. Curmi, S. Akimoto, S. Iwata, 2008, Nature Structural &Molecular Biology.

Equilibration of tyrosyl radicals (Y356•, Y731•, Y730•) in the radical propagation pathway of the Escherichia coli class Ia ribonucleotide reductase.

R. Griffin, K. Yokoyama, J. Stubbe, 2011, Journal of the American Chemical Society.

Biosynthesis of linkage units for teichoic acids in gram-positive bacteria: distribution of related enzymes and their specificities for UDP-sugars and lipid-linked intermediates

K. Yokoyama, H. Mizuguchi, K. Yokoyama, 1989, Journal of bacteriology.

Resolving stepping rotation in Thermus thermophilus H+-ATPase/synthase with an essentially drag-free probe

K. Yokoyama, H. Noji, K. Adachi, 2011, Nature communications.

Function of the diiron cluster of Escherichia coli class Ia ribonucleotide reductase in proton-coupled electron transfer.

K. Yokoyama, C. Krebs, J. Bollinger, 2013, Journal of the American Chemical Society.

A hot oxidant, 3-NO2Y122 radical, unmasks conformational gating in ribonucleotide reductase.

U. Uhlin, K. Yokoyama, J. Stubbe, 2010, Journal of the American Chemical Society.

Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox-active tyrosines in ribonucleotide reductase.

U. Uhlin, K. Yokoyama, J. Stubbe, 2010, Journal of the American Chemical Society.

Distribution of mannosamine and mannosaminuronic acid among cell walls of Bacillus species

K. Yokoyama, T. Kawamura, H. Arakawa, 1982, Journal of bacteriology.

Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy.

K. Yokoyama, T. Eguchi, F. Kudo, 2008, Biochemistry.

Extended longevity of Caenorhabditis elegans by knocking in extra copies of hsp70F, a homolog of mot‐2 (mortalin)/mthsp70/Grp75

R. Hosono, K. Yokoyama, R. Wadhwa, 2002, FEBS letters.

Biosynthesis of poly(galactosylglycerol phosphate) in Bacillus coagulans.

K. Yokoyama, Y. Araki, E. Ito, 1987, European journal of biochemistry.

Structural and biosynthetic studies on linkage region between poly(galactosylglycerol phosphate) and peptidoglycan in Bacillus coagulans.

K. Yokoyama, Y. Araki, S. Kaya, 1983, Biochemical and Biophysical Research Communications - BBRC.

Biosynthesis of 2-Deoxystreptamine by Three Crucial Enzymes in Streptomyces fradiae NBRC 12773

K. Yokoyama, T. Eguchi, K. Kakinuma, 2005, The Journal of Antibiotics.

The function of galactosyl phosphorylpolyprenol in biosynthesis of lipoteichoic acid in Bacillus coagulans.

K. Yokoyama, Y. Araki, E. Ito, 1988, European journal of biochemistry.

Thermostable farnesyl diphosphate synthase of Bacillus stearothermophilus: molecular cloning, sequence determination, overproduction, and purification.

T. Koyama, K. Yokoyama, T. Nishino, 1993, Journal of biochemistry.

A Chemically Competent Thiosulfuranyl Radical on the Escherichia coli Class III Ribonucleotide Reductase

Jiahao Chen, R. Griffin, K. Yokoyama, 2014, Journal of the American Chemical Society.

In vivo fluorescent adenosine 5'-triphosphate (ATP) imaging of Drosophila melanogaster and Caenorhabditis elegans by using a genetically encoded fluorescent ATP biosensor optimized for low temperatures.

T. Uemura, A. Tsubouchi, Y. Harada, 2013, Analytical chemistry.

Cryo-EM studies of the rotary H+-ATPase/synthase from Thermus thermophilus

K. Yokoyama, K. Mitsuoka, A. Nakanishi, 2019, Biophysics and physicobiology.

Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus

K. Yokoyama, K. Mitsuoka, A. Nakanishi, 2018, Nature Communications.

Mechanical inhibition of isolated Vo from V/A-ATPase for proton conductance

K. Namba, K. Yokoyama, K. Mitsuoka, 2020, eLife.

Dodecamer rotor ring defines H+/ATP ratio for ATP synthesis of prokaryotic V-ATPase from Thermus thermophilus

Kazutoshi Tani, Masasuke Yoshida, Masahiro Nakano, 2007, Proceedings of the National Academy of Sciences.

ATP Hydrolysis and Synthesis of a Rotary Motor V-ATPase from Thermus thermophilus*

Masasuke Yoshida, K. Yokoyama, Masahiro Nakano, 2008, Journal of Biological Chemistry.

Identification of chemical compounds as an inhibitor of mitochondrial ATP synthesis, leading to an increased stress resistance and an extended lifespan in C. elegans.

K. Yokoyama, J. Kishikawa, M. Fujikawa, 2020, Biochimica et biophysica acta. Bioenergetics.

General anesthetics cause mitochondrial dysfunction and reduction of intracellular ATP levels

K. Yokoyama, A. Nakanishi, T. Tanabe, 2018, PloS one.

Molecular cloning of genes encoding major two subunits of a eubacterial V-type ATPase from Thermus thermophilus.

K. Yokoyama, T. Date, T. Oshima, 1991, Biochimica et biophysica acta.

V-ATPase of Thermus thermophilus Is Inactivated during ATP Hydrolysis but Can Synthesize ATP*

Masasuke Yoshida, E. Muneyuki, M. Ishida, 1998, The Journal of Biological Chemistry.

Thermus thermophilus membrane-associated ATPase. Indication of a eubacterial V-type ATPase.

K. Yokoyama, T. Oshima, M. Yoshida, 1990, The Journal of biological chemistry.

Cryptic phosphorylation in nucleoside natural product biosynthesis

K. Yokoyama, Anyarat Thanapipatsiri, Matthew M. Draelos, 2020, Nature Chemical Biology.

Reconstitution in Vitro of V1 Complex of Thermus thermophilus V-ATPase Revealed That ATP Binding to the A Subunit Is Crucial for V1 Formation*

Masasuke Yoshida, K. Yokoyama, H. Imamura, 2006, Journal of Biological Chemistry.

Rotation of the Proteolipid Ring in the V-ATPase*

Hiromi Imamura, Masasuke Yoshida, Masahiro Nakano, 2003, Journal of Biological Chemistry.

Evidence for rotation of V1-ATPase

Hiroyuki Noji, Hiromi Imamura, Masasuke Yoshida, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Rotation, Structure, and Classification of Prokaryotic V-ATPase

K. Yokoyama, H. Imamura, 2005, Journal of bioenergetics and biomembranes.

Rotation scheme of V1-motor is different from that of F1-motor.

Masasuke Yoshida, K. Yokoyama, H. Imamura, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Subunit Arrangement in V-ATPase from Thermus thermophilus*

Masasuke Yoshida, K. Nagata, K. Yokoyama, 2003, Journal of Biological Chemistry.

Mechanism of ATP hydrolysis dependent rotation of ATP synthases

K. Yokoyama, K. Mitsuoka, J. Kishikawa, 2022, bioRxiv.

Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases

K. Yokoyama, J. Kishikawa, A. Furuta, 2022, Nature Communications.

Structural snapshots of V/A-ATPase reveal a new paradigm for rotary catalysis

K. Yokoyama, S. Saeki, J. Kishikawa, 2021, bioRxiv.

Rotation of artificial rotor axles in rotary molecular motors

R. Iino, K. Yokoyama, H. Noji, 2016, Proceedings of the National Academy of Sciences.

GraDeR: Membrane Protein Complex Preparation for Single-Particle Cryo-EM.

H. Stark, Y. Fujiyoshi, K. Shinzawa-Itoh, 2015, Structure.

Structure of Prokaryotic V-Type ATPase/Synthase

K. Yokoyama, J. Kishikawa, 2014 .

Crystal structure of A 3 B 3 complex of V-ATPase from Thermus thermophilus This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited.Thislicensedoesnot pe

Koji Nagata, Megan J. Maher, S. Akimoto, 2009 .

Leu309 Plays a Critical Role in the Encapsulation of Substrate Protein into the Internal Cavity of GroEL*

H. Taguchi, Masasuke Yoshida, K. Yokoyama, 2006, Journal of Biological Chemistry.

Unnatural amino acids: better than the real things?

K. Yokoyama, J. Stubbe, E. Minnihan, 2009, F1000 biology reports.

Crystallization of the chaperonin GroEL-GroES complex from Thermus thermophilus HB8.

H. Taguchi, Masasuke Yoshida, S. Iwata, 2003, Acta crystallographica. Section D, Biological crystallography.

The reconstituted alpha 3 beta 3 delta complex of the thermostable F1-ATPase.

K. Yokoyama, M. Yoshida, T. Hisabori, 1989, The Journal of biological chemistry.

Reconstitution of Vacuolar-type Rotary H+-ATPase/Synthase from Thermus thermophilus*♦

K. Yokoyama, J. Kishikawa, 2012, The Journal of Biological Chemistry.

Rotary mechanism of V/A-ATPases—how is ATP hydrolysis converted into a mechanical step rotation in rotary ATPases?

K. Yokoyama, 2023, Frontiers in Molecular Biosciences.

Length specificity and polymerization mechanism of (1,3)-β-D-glucan synthase in fungal cell wall biosynthesis.

K. Yokoyama, Mi Jung Kim, Jiyong Hong, 2020, Biochemistry.

Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus

K. Yokoyama, K. Mitsuoka, A. Nakanishi, 2018, Nature Communications.

Single-molecule Analysis of Inhibitory Pausing States of V1-ATPase*

K. Yokoyama, H. Noji, Masahiro Nakano, 2012, The Journal of Biological Chemistry.

Engineering of New Pneumocandin Side-Chain Analogues from Glarea lozoyensis by Mutasynthesis and Evaluation of Their Antifungal Activity.

K. Yokoyama, Xingzhong Liu, G. Bills, 2016, ACS chemical biology.

F-subunit reinforces torque generation in V-ATPase

K. Yokoyama, H. Noji, A. Nakanishi, 2014, European Biophysics Journal.

Structural basis of unisite catalysis of bacterial F0F1-ATPase

K. Yokoyama, K. Mitsuoka, A. Nakanishi, 2022, PNAS nexus.

Characterization of Acyl Carrier Protein-Dependent Glycosyltransferase in Mitomycin C Biosynthesis.

K. Yokoyama, Hai Nguyen, 2019, Biochemistry.

Involvement of Two Distinct N‐Acetylglucosaminyltransferases and a Dual‐Function Deacetylase in Neomycin Biosynthesis

K. Yokoyama, T. Eguchi, F. Kudo, 2008, Chembiochem : a European journal of chemical biology.

[Two rotary molecular motors, V-ATPase and F0F1].

K. Yokoyama, H. Imamura, 2007, Seikagaku. The Journal of Japanese Biochemical Society.

Common Evolutionary Origin for the Rotor Domain of Rotary Atpases and Flagellar Protein Export Apparatus

K. Namba, K. Yokoyama, K. Imada, 2013, PloS one.

Equilibration of Tyrosyl Radicals (Y[• over 356], Y[• over 731], Y[• over 730]) in the Radical Propagation Pathway of the Escherichia coli Class Ia Ribonucleotide Reductase

R. Griffin, K. Yokoyama, J. Stubbe, 2011 .

Faculty Opinions recommendation of Cryo-EM structure of a fungal mitochondrial calcium uniporter.

K. Yokoyama, 2018, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase

F. Asturias, K. Yokoyama, E. Brignole, 2011, Proceedings of the National Academy of Sciences of the United States of America.

Equilibration of tyrosyl radicals (Y356•, Y731•, Y730•) in the radical propagation pathway of the Escherichia coli class Ia ribonucleotide reductase.

R. Griffin, K. Yokoyama, J. Stubbe, 2011, Journal of the American Chemical Society.

Mechanism of ATP hydrolysis dependent rotation of bacterial ATP synthase

K. Yokoyama, K. Mitsuoka, J. Kishikawa, 2023, Nature communications.

Molecular Basis of ADP Inhibition of Vacuolar (V)-type ATPase/Synthase*

K. Yokoyama, A. Nakanishi, M. Tamakoshi, 2013, The Journal of Biological Chemistry.

Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5'-diphosphate in the presence or absence of reductant.

R. Griffin, K. Yokoyama, J. Stubbe, 2009, Biochemistry.