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Data Science and PDBj Activities

2018 Seibutsu Butsuri  
doi:10.2142/biophys.58.071 fatcat:l6sbtw46hbbaxc3bapznxqxvaq

Structural atlas of dynein motors at atomic resolution

Akiyuki Toda, Hideaki Tanaka, Genji Kurisu
2018 Biophysical Reviews  
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 studies of every component of dynein and summarize them as a structural atlas that classifies the
more » ... cytoplasmic and axonemal dyneins. Based on our review of all dynein structures in the Protein Data Bank, we raise two important points for understanding the two types of dynein motor and discuss the potential prospects of future structural studies.
doi:10.1007/s12551-018-0402-y pmid:29478092 pmcid:PMC5899744 fatcat:5526c7m7sjf7nkgu3piu7dhr2a

Photosynthetic Electron Transfer around Cytochrome b6f Complex Based on its Crystal Structure

2004 Seibutsu Butsuri  
Table 1 . 1 Photosynthetic Electron Transfer around Cytochrome b 6 f Complex Based on its Crystal Structure Genji KURISU Department of Life Sciences, Graduate School of Arts and Sciences, The University  ... 
doi:10.2142/biophys.44.130 fatcat:hup3c5e6xfev5b7hrodyavndkq

Evolution of Photosynthesis: Time-Independent Structure of the Cytochromeb6fComplex†

William A. Cramer, Huamin Zhang, Jiusheng Yan, Genji Kurisu, Janet L. Smith
2004 Biochemistry  
Structures of the cytochrome b 6 f complex obtained from the thermophilic cyanobacterium Mastigocladus laminosus and the green alga Chlamydomonas reinhardtii, whose appearance in evolution is separated by 10 9 years, are almost identical. Two monomers with a molecular weight of 110 000, containing eight subunits and seven natural prosthetic groups, are separated by a large lipid-containing "quinone exchange cavity". A unique heme, heme x, that is five-coordinated and high-spin, with no strong
more » ... eld ligand, occupies a position close to intramembrane heme b n . This position is filled by the n-side bound quinone, Q n , in the cytochrome bc 1 complex of the mitochondrial respiratory chain. The structure and position of heme x suggest that it could function in ferredoxin-dependent cyclic electron transport as well as being an intermediate in a quinone cycle mechanism for electron and proton transfer. The significant differences between the cyanobacterial and algal structures are as follows. (i) On the n-side, a plastoquinone molecule is present in the quinone exchange cavity in the cyanobacterial complex, and a sulfolipid is bound in the algal complex at a position corresponding to a synthetic DOPC lipid molecule in the cyanobacterial complex. (ii) On the p-side, in both complexes a quinone analogue inhibitor, TDS, passes through a portal that separates the large cavity from a niche containing the Fe 2 S 2 cluster. However, in the cyanobacterial complex, TDS is in an orientation that is the opposite of its position in the algal structure and bc 1 complexes, so its headgroup in the M. laminosus structure is 20 Å from the Fe 2 S 2 cluster. † The studies reported in this review were supported by NIH Grant GMS-38323 (W.A.C.) and a fellowship from The Japanese Ministry of Education (G.K.).
doi:10.1021/bi049444o pmid:15147175 fatcat:fkjwpz4z4rbkpjbjtues6glepq

Crystallography in Biology; Visualization of Biological Process

Ikuko MIYAHARA, Noriyuki IGARASHI, Nobutada TANAKA, Genji KURISU
2014 Nihon Kessho Gakkaishi  
, Ikuko MIYAHARA, Noriyuki IGARASHI, Nobutada TANAKA and Genji KURISU: Crystallography in Biology; Visualization of Biological Process  ... 
doi:10.5940/jcrsj.56.223 fatcat:o73sqqgwwbdabndpbwkbm4rcvq

The 2.8-Å Crystal Structure of the Dynein Motor Domain

Takahide Kon, Takuji Oyama, Rieko Shimo-Kon, Kazuo Sutoh, Genji Kurisu
2012 Biophysical Journal  
Kurisu 1 . 1 Osaka Univ, Osaka, Japan, 2 Waseda Univ, Tokyo, Japan.  ...  the coiled-coil and dynein's affinity for its track. 1864-Pos Board B634 The 2.8-Å Crystal Structure of the Dynein Motor Domain Takahide Kon 1 , Takuji Oyama 1 , Rieko Shimo-Kon 1 , Kazuo Sutoh 2 , Genji  ... 
doi:10.1016/j.bpj.2011.11.2007 fatcat:r3fhl2gdlvdnjcknzdwnbbu3iu

Continuum Mechanical Parameterisation of Cytoplasmic Dynein from Atomistic Simulation

Benjamin S. Hanson, Shinji Iida, Daniel J. Read, Oliver G. Harlen, Genji Kurisu, Haruki Nakamura, Sarah A. Harris
2020 Methods  
Cytoplasmic dynein is responsible for intra-cellular transport in eukaryotic cells. Using Fluctuating Finite Element Analysis (FFEA), a novel algorithm that represents proteins as continuum viscoelastic solids subject to thermal noise, we are building computational tools to study the mechanics of these molecular machines. Here we present a methodology for obtaining the material parameters required to represent the flexibility of cytoplasmic dynein within FFEA from atomistic molecular dynamics
more » ... D) simulations, and show that this continuum representation is sufficient to capture the principal dynamic properties of the motor.
doi:10.1016/j.ymeth.2020.01.021 pmid:32007556 fatcat:cilnlg2otrdrxmr3bdev2lxw4a

Molecular Dynamics Simulations of Dynein Motor Domain in Explicit Water

Narutoshi Kamiya, Tadaaki Mashimo, Yu Takano, Takahide Kon, Genji Kurisu, Haruki Nakamura
2014 Biophysical Journal  
Kurisu 1 , Haruki Nakamura 1 . 1 Osaka University, Osaka, Japan, 2 Japan Biological Informatics Consortium, Tokyo, Japan, 3 JST, CREST, Saitama, Japan, 4 Hosei University, Tokyo, Japan, 5 JST, PRESTO,  ...  challenging than thus far imagined. 3362-Pos Board B90 Molecular Dynamics Simulations of Dynein Motor Domain in Explicit Water Narutoshi Kamiya 1 , Tadaaki Mashimo 2 , Yu Takano 1,3 , Takahide Kon 4,5 , Genji  ... 
doi:10.1016/j.bpj.2013.11.3678 fatcat:r4ijn4qftzgavjleutahm5wevu

PDBx/mmCIF Format Mandatory for Protein Data Bank Deposition

Gert-Jan BEKKER, Takahiro KUDOU, Yasuyo IKEGAWA, Reiko YAMASHITA, Genji KURISU
2019 Nihon Kessho Gakkaishi  
Gert-Jan BEKKER, Takahiro KUDOU, Yasuyo IKEGAWA, Reiko YAMASHITA and Genji KURISU: PDBx/mmCIF Format Mandatory for Protein Data Bank Deposition 2018 年 11 月 2 日,英国 Cambridge の Madingley Hall に おいて開催された  ... 
doi:10.5940/jcrsj.61.159 fatcat:sfp7xwqddvh6vpvk4o4wqxojya

Visualization of Chemical Reactions by Crystallography

Shin-ichi ADACHI, Hidehiro UEKUSA, Tomoji OZEKI, Masaki KAWANO, Genji KURISU
2013 Nihon Kessho Gakkaishi  
doi:10.5940/jcrsj.55.1 fatcat:qadnxvmxnjblhognfi4rgi6sdi

Atomic Structure of Plant Glutamine Synthetase

Hideaki Unno, Tatsuya Uchida, Hajime Sugawara, Genji Kurisu, Tatsuo Sugiyama, Tomoyuki Yamaya, Hitoshi Sakakibara, Toshiharu Hase, Masami Kusunoki
2006 Journal of Biological Chemistry  
Plants provide nourishment for animals and other heterotrophs as the sole primary producer in the food chain. Glutamine synthetase (GS), one of the essential enzymes for plant autotrophy catalyzes the incorporation of ammonia into glutamate to generate glutamine with concomitant hydrolysis of ATP, and plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development. Elucidation of the atomic structure
more » ... f higher plant GS is important to understand its detailed reaction mechanism and to obtain further insight into plant productivity and agronomical utility. Here we report the first crystal structures of maize (Zea mays L.) GS. The structure reveals a unique decameric structure that differs significantly from the bacterial GS structure. Higher plants have several isoenzymes of GS differing in heat stability and catalytic properties for efficient responses to variation in the environment and nutrition. A key residue responsible for the heat stability was found to be Ile-161 in GS1a. The three structures in complex with substrate analogues, including phosphinothricin, a widely used herbicide, lead us to propose a mechanism for the transfer of phosphate from ATP to glutamate and to interpret the inhibitory action of phosphinothricin as a guide for the development of new potential herbicides. * This work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. □ S The on-line version of this article (available at contains supplemental Figs. S1 and S2. The atomic coordinates and structure factors (code 2D3A, 2D3B, and 2D3C) have been deposited in the Protein 7 The abbreviations used are: GS, glutamine synthetase; MetSox-P, methionine sulfoximine phosphate; PEG, polyethylene glycol; MetSox, methionine sulfoximine; PPT-P, phosphinothricin phosphate; AMPPNP, adenylyl imidodiphosphate; PPT, phosphinothricin; NCS, non-crystallographic symmetry. Downloaded from FIGURE 4. Representation of the interactions between enzyme and substrate analogues. a, stick models for the interaction of the enzyme with AMPPNP and MetSox. Carbon, oxygen, nitrogen, phosphorus, and sulfur atoms are colored gray, red, blue, salmon, and yellow, respectively. Three Mn 2ϩ are indicated in pink spheres. Dotted lines designate hydrogen bonds and coordination bonds to Mn 2ϩ ions. Residues without dotted lines have hydrophobic interactions with the substrate. b, stick models for the interaction of the enzyme with ADP and MetSox. c, stick models for the interaction of the enzyme with ADP and PPT-P.
doi:10.1074/jbc.m601497200 pmid:16829528 fatcat:jul7tms6g5bj7jjmhiymzkji24

Structural Studies on the Electron Transfer Complex from Higher Plant

2001 Nihon Kessho Gakkaishi  
After the single structures of ferredoxin and ferredoxin-NADP+ reductase have been reported, no complex structure of them was reported. Here we report the crystallization of the electron transfer complex between ferredoxin and ferredoxin-NADP+ reductase from maize leaf and the structure analysis of this complex at 2.59 A resolution. The structures of ferredoxin and ferredoxin-NADP+ reductase in this complex state differ from the structures of single states. The complex formation not only
more » ... nes optimal orientation of the two proteins, but also contributes to modulation of the enzymatic properties.
doi:10.5940/jcrsj.43.399 fatcat:esvnmp4zxzdl3gmz27u2u3kjrq

A New Era in Crystallography; X-ray Free Electron Laser

2014 Nihon Kessho Gakkaishi  
Genji KURISU and Eiji NISHIBORI: A New Era in Crystallography; X-ray Free Electron Laser , 100 . 100 , X , . IUCr , ICSU UNESCO , , 2014 . , 100 , , , . , , 2014 .  ... 
doi:10.5940/jcrsj.56.3 fatcat:iy3yybi3inebxlqzzktukz5kma

Structural basis for chiral substrate recognition by two 2,3-butanediol dehydrogenases

Masato Otagiri, Sadaharu Ui, Yuhsuke Takusagawa, Takashi Ohtsuki, Genji Kurisu, Masami Kusunoki
2009 FEBS Letters  
2,3-Butanediol dehydrogenase (BDH) catalyzes the NAD-dependent redox reaction between acetoin and 2,3-butanediol. There are three types of homologous BDH, each stereospecific for both substrate and product. To establish how these homologous enzymes possess differential stereospecificities, we determined the crystal structure of L-BDH with a bound inhibitor at 2.0 Å. Comparison with the inhibitor binding mode of meso-BDH highlights the role of a hydrogen-bond from a conserved Trp residue 192 .
more » ... te-directed mutagenesis of three active site residues of meso-BDH, including Trp 190 , which corresponds to Trp 192 of L-BDH, converted its stereospecificity to that of L-BDH. This result confirms the importance of conserved residues in modifying the stereospecificity of homologous enzymes.
doi:10.1016/j.febslet.2009.11.068 pmid:19941855 fatcat:jdk4zayhnrhnxjz65okfcjk5f4

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

Stephen K. Burley, Genji Kurisu, John L. Markley, Haruki Nakamura, Sameer Velankar, Helen M. Berman, Andrej Sali, Torsten Schwede, Jill Trewhella
2017 Structure  
doi:10.1016/j.str.2017.08.001 pmid:28877501 pmcid:PMC5821105 fatcat:ezsxdvjksvhhpotipe4bgwhl7a
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