Search results for: Genji Kurisu

Items from 1 to 20 out of 47 results

article

Crystal structure of the stalk region of axonemal inner‐arm dynein‐d reveals unique features in the coiled‐coil and microtubule‐binding domain

Seolmin Ko, Akiyuki Toda, Hideaki Tanaka, Jian Yu, more

Axonemal dynein is an ATP‐dependent microtubular motor protein responsible for cilia and flagella beating, and its dysfunction can cause diseases such as primary ciliary dyskinesia and sperm dysmotility. Despite its biological importance, structure‐based mechanisms underlying axonemal dynein motors remain unclear. Here, we determined the X‐ray crystal structure of the human inner‐arm dynein‐d (DNAH1)...

article

Crystal structure and reaction mechanism of a bacterial Mg‐dechelatase homolog from the Chloroflexi Anaerolineae

Debayan Dey, Masayoshi Nishijima, Ryouichi Tanaka, Genji Kurisu, more

Protein Science > 31 > 10 > n/a - n/a

Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg‐dechelatase enzyme encoded by Stay‐Green (SGR). The reaction mechanism of SGR...

article

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Gert‐Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, more

Protein Science > 31 > 1 > 173 - 186

Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB) has accepted, processed and distributed experimentally determined biological macromolecular structures for 20 years. During that time, we have continuously made major improvements to our query search interface of PDBj Mine 2, the BMRBj web interface, and EM Navigator for PDB/BMRB/EMDB entries. PDBj also serves...

article

Structural basis for thioredoxin isoform‐based fine‐tuning of ferredoxin‐thioredoxin reductase activity

Linda Juniar, Hideaki Tanaka, Keisuke Yoshida, Toru Hisabori, more

Protein Science > 29 > 12 > 2538 - 2545

Photosynthetic electron transport occurs on the thylakoid membrane of chloroplasts. Ferredoxin (Fd), the final acceptor in the electron transport chain, distributes electrons to several Fd‐dependent enzymes including Fd‐thioredoxin reductase (FTR). A cascade from Fd to FTR further reduces Thioredoxin (Trx), which tunes the activity of target metabolic enzymes eventually in a light‐dependent manner...

article

Copper–Oxygen Dynamics in the Tyrosinase Mechanism

Nobutaka Fujieda, Kyohei Umakoshi, Yuta Ochi, Yosuke Nishikawa, more

Angewandte Chemie International Edition > 59 > 32 > 13385 - 13390

The dinuclear copper enzyme, tyrosinase, activates O₂ to form a (μ‐η²:η²‐peroxido)dicopper(II) species, which hydroxylates phenols to catechols. However, the exact mechanism of phenolase reaction in the catalytic site of tyrosinase is still under debate. We herein report the near atomic resolution X‐ray crystal structures of the active tyrosinases with substrate l‐tyrosine. At their catalytic sites,...

article

Copper–Oxygen Dynamics in the Tyrosinase Mechanism

Nobutaka Fujieda, Kyohei Umakoshi, Yuta Ochi, Yosuke Nishikawa, more

Angewandte Chemie > 132 > 32 > 13487 - 13492

article

Cupin Variants as a Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes

Nobutaka Fujieda, Haruna Ichihashi, Miho Yuasa, Yosuke Nishikawa, more

Angewandte Chemie International Edition > 59 > 20 > 7717 - 7720

Cupin superfamily proteins (TM1459) work as a macromolecular ligand framework with a double‐stranded β‐barrel structure ligating to a Cu ion through histidine side chains. Variegating the first coordination sphere of TM1459 revealed that H52A and H54A/H58A mutants effectively catalyzed the diastereo‐ and enantioselective Michael addition reaction of nitroalkanes to an α,β‐unsaturated ketone. Moreover,...

article

Cupin Variants as a Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes

Nobutaka Fujieda, Haruna Ichihashi, Miho Yuasa, Yosuke Nishikawa, more

Angewandte Chemie > 132 > 20 > 7791 - 7794

article

Electron transport pathways in isolated chromoplasts from Narcissus pseudonarcissus L.

Magda Grabsztunowicz, Paula Mulo, Frauke Baymann, Risa Mutoh, more

The Plant Journal > 99 > 2 > 245 - 256

During daffodil flower development, chloroplasts differentiate into photosynthetically inactive chromoplasts having lost functional photosynthetic reaction centers. Chromoplasts exhibit a respiratory activity reducing oxygen to water and generating ATP. Immunoblots revealed the presence of the plastid terminal oxidase (PTOX), the NAD(P)H dehydrogenase (NDH) complex, the cytochrome b₆f complex, ATP...

article

Structural atlas of dynein motors at atomic resolution

Akiyuki Toda, Hideaki Tanaka, Genji Kurisu

Biophysical Reviews > 2018 > 10 > 2 > 677-686

Dynein motors are biologically important bio-nanomachines, and many atomic resolution structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy. This review provides a historical perspective of structural studies of cytoplasmic and axonemal dynein including accessory proteins. We describe representative structural...

article

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

Akira R. Kinjo, Gert‐Jan Bekker, Hiroshi Wako, Shigeru Endo, more

Protein Science > 27 > 1 > 95 - 102

The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures. In addition to archiving the PDB data in collaboration with the other wwPDB partners, PDBj also provides a wide range of original and unique services and tools, which are continuously improved and updated...

article

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

Stephen K. Burley, Genji Kurisu, John L. Markley, Haruki Nakamura, more

Structure > 2017 > 25 > 9 > 1317-1318

Burley et al. (leadership of the Worldwide PDB [wwPDB] Partnership [wwpdb.org] and the wwPDB Integrative/Hybrid Methods Task Force) announce public release of a prototype system for depositing integrative/hybrid structural models, PDB-Development (PDB-Dev; https://pdb-dev.wwpdb.org).

article

Dynamics and energetics of cyanobacterial photosystem I:ferredoxin complexes in different redox states

Pierre Sétif, Risa Mutoh, Genji Kurisu

Biochimica et Biophysica Acta (BBA) - Bioenergetics > 2017 > 1858 > 7 > 483-496

Fast turnover of ferredoxin/Fd reduction by photosystem-I/PSI requires that it dissociates rapidly after it has been reduced by PSI:Fd intracomplex electron transfer. The rate constants of Fd dissociation from PSI have been determined by flash-absorption spectroscopy with different combinations of cyanobacterial PSIs and Fds, and different redox states of Fd and of the terminal PSI acceptor (F_AF_B)...

article

Association of Ferredoxin:NADP⁺ oxidoreductase with the photosynthetic apparatus modulates electron transfer in Chlamydomonas reinhardtii

Laura Mosebach, Claudia Heilmann, Risa Mutoh, Philipp Gäbelein, more

Photosynthesis Research > 2017 > 134 > 3 > 291-306

Ferredoxins (FDX) and the FDX:NADP⁺ oxidoreductase (FNR) represent a key junction of electron transport downstream of photosystem I (PSI). Dynamic recruitment of FNR to the thylakoid membrane has been considered as a potential mechanism to define the fate of photosynthetically derived electrons. In this study, we investigated the functional importance of the association of FNR with the photosynthetic...

article

Gallium ferredoxin as a tool to study the effects of ferredoxin binding to photosystem I without ferredoxin reduction

Clara Mignée, Risa Mutoh, Anja Krieger-Liszkay, Genji Kurisu, more

Photosynthesis Research > 2017 > 134 > 3 > 251-263

Reduction of ferredoxin by photosystem I (PSI) involves the [4Fe–4S] clusters F_A and F_B harbored by PsaC, with F_B being the direct electron transfer partner of ferredoxin (Fd). Binding of the redox-inactive gallium ferredoxin to PSI was investigated by flash-absorption spectroscopy, studying both the P700⁺ decay and the reduction of the native iron Fd in the presence of Fd_Ga. Fd_Ga binding resulted...

article

Energetic basis on interactions between ferredoxin and ferredoxin NADP+ reductase at varying physiological conditions

Misaki Kinoshita, Ju Yaen Kim, Satoshi Kume, Yuxi Lin, more

Biochemical and Biophysical Research Communications > 2017 > 482 > 4 > 909-915

In spite of a number of studies to characterize ferredoxin (Fd):ferredoxin NADP⁺ reductase (FNR) interactions at limited conditions, detailed energetic investigation on how these proteins interact under near physiological conditions and its linkage to FNR activity are still lacking.We herein performed systematic Fd:FNR binding thermodynamics using isothermal titration calorimetry (ITC) at distinct...

article

Structural basis for the isotype-specific interactions of ferredoxin and ferredoxin: NADP⁺ oxidoreductase: an evolutionary switch between photosynthetic and heterotrophic assimilation

Fumio Shinohara, Genji Kurisu, Guy Hanke, Caroline Bowsher, more

Photosynthesis Research > 2017 > 134 > 3 > 281-289

In higher plants, ferredoxin (Fd) and ferredoxin-NADP⁺ reductase (FNR) are each present as distinct isoproteins of photosynthetic type (leaf type) and non-photosynthetic type (root type). Root-type Fd and FNR are considered to facilitate the electron transfer from NADPH to Fd in the direction opposite to that occurring in the photosynthetic processes. We previously reported the crystal structure of...

article

Structural Change in the Dynein Stalk Region Associated with Two Different Affinities for the Microtubule

Yosuke Nishikawa, Momoko Inatomi, Haruka Iwasaki, Genji Kurisu

Journal of Molecular Biology > 2016 > 428 > 9(PB) > 1886-1896

Dynein is a large microtubule-based motor complex that requires tight coupling of intra-molecular ATP hydrolysis with the generation of mechanical force and track-binding activity. However, the microtubule-binding domain is structurally separated by about 15nm from the nucleotide-binding sites by a coiled-coil stalk. Thus, long-range two-way communication is necessary for coordination between the...

article

Physicochemical nature of interfaces controlling ferredoxin NADP+ reductase activity through its interprotein interactions with ferredoxin

Misaki Kinoshita, Ju yaen Kim, Satoshi Kume, Yukiko Sakakibara, more

Biochimica et Biophysica Acta (BBA) - Bioenergetics > 2015 > 1847 > 10 > 1200-1211

Although acidic residues of ferredoxin (Fd) are known to be essential for activities of various Fd-dependent enzymes, including ferredoxin NADP⁺ reductase (FNR) and sulfite reductase (SiR), through electrostatic interactions with basic residues of partner enzymes, non-electrostatic contributions such as hydrophobic forces remain largely unknown. We herein demonstrated that intermolecular hydrophobic...

article

Direct evidence for the atovaquone action on the Plasmodium cytochrome bc1 complex

Josephine E. Siregar, Genji Kurisu, Tamaki Kobayashi, Motomichi Matsuzaki, more

Parasitology International > 2015 > 64 > 3 > 295-300

Atovaquone, a coenzyme Q analogue has been indicated to specifically target the cytochrome bc₁ complex of the mitochondrial respiratory chain in the malarial parasite and other protozoan. Various mutations in the quinone binding site of the cytochrome b gene of Plasmodium spp. such as M133I, L144S, L271V, K272R, Y268C, Y268S, Y268N, and V284F are suggesting to associate with resistance to atovaquone...

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FERREDOXIN (9)
ELECTRON TRANSFER COMPLEX (5)
ELECTRON TRANSFER (4)
PHOTOSYNTHESIS (4)
X-RAY CRYSTALLOGRAPHY (4)
DYNEIN (3)
ACTIVE SITE DYNAMICS (2)
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COPPER (2)
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CUPIN (2)
CYTOSKELETAL MOTOR PROTEIN (2)
DIOXYGEN ACTIVATION (2)
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FERREDOXIN-NADP+ REDUCTASE (2)
FERREDOXIN: NADP(H) OXIDOREDUCTASE (2)
FERREDOXIN–NADP+ REDUCTASE (2)
LEAF- AND ROOT-TYPE ISOFORMS (2)
PDB (2)
PROTEIN STRUCTURES (2)
REDOX POTENTIAL (2)
REDUCTIVE ASSIMILATION (2)
STALK COILED COIL (2)
TYROSINASE (2)
X-RAY CRYSTAL STRUCTURE (2)
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ARTIFICIAL METALLOENZYMES (1)
ASSOCIATION AND DISSOCIATION KINETICS (1)
ATOVAQUONE-RESISTANCE (1)
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BUTANEDIOL DEHYDROGENASE (1)
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CHLAMYDOMONAS REINHARDTII (1)
CHLOROPHYLL A (1)
CHLOROPHYLL DEGRADATION (1)
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GLYCOSIDE HYDROLASE FAMILY 116 (1)
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INFONA - science communication portal

Search results for: Genji Kurisu

Crystal structure of the stalk region of axonemal inner‐arm dynein‐d reveals unique features in the coiled‐coil and microtubule‐binding domain

Crystal structure and reaction mechanism of a bacterial Mg‐dechelatase homolog from the Chloroflexi Anaerolineae

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

Structural basis for thioredoxin isoform‐based fine‐tuning of ferredoxin‐thioredoxin reductase activity

Copper–Oxygen Dynamics in the Tyrosinase Mechanism

Copper–Oxygen Dynamics in the Tyrosinase Mechanism

Cupin Variants as a Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes

Cupin Variants as a Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes

Electron transport pathways in isolated chromoplasts from Narcissus pseudonarcissus L.

Structural atlas of dynein motors at atomic resolution

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

Dynamics and energetics of cyanobacterial photosystem I:ferredoxin complexes in different redox states

Association of Ferredoxin:NADP⁺ oxidoreductase with the photosynthetic apparatus modulates electron transfer in Chlamydomonas reinhardtii

Gallium ferredoxin as a tool to study the effects of ferredoxin binding to photosystem I without ferredoxin reduction

Energetic basis on interactions between ferredoxin and ferredoxin NADP+ reductase at varying physiological conditions

Structural basis for the isotype-specific interactions of ferredoxin and ferredoxin: NADP⁺ oxidoreductase: an evolutionary switch between photosynthetic and heterotrophic assimilation

Structural Change in the Dynein Stalk Region Associated with Two Different Affinities for the Microtubule

Physicochemical nature of interfaces controlling ferredoxin NADP+ reductase activity through its interprotein interactions with ferredoxin

Direct evidence for the atovaquone action on the Plasmodium cytochrome bc1 complex

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