Journal of the Crystallographic Society of Japan
Volume 50 (6), 2008.
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J. Cryst. Soc. Jpn., 50(6), 329-334 (2008).
The Structural Basis for an Essential Subunit Interaction in Influenza Virus RNA Polymerase
Eiji OBAYASHI1 , Hisashi YOSHIDA2 and Sam-Yong PARK3
Affilication: 1, 2, 3Protein Design Laboratory, Yokohama City University
Address: 1, 2, 31-7-29 Suehiro, Tsurumi, Yokohama 230-0045, Japan
E-Mail: 1eijioba(%)tsurumi.yokohama-cu.ac.jp, 2, 3park(%)tsurumi.yokohama-cu.ac.jp

Influenza A virus is a major human and animal pathogen with the potential to cause catastrophic loss of life. The virus reproduces rapidly, mutates frequently, and occasionally crosses species barriers. The recent emergence in Asia of avian influenza related to highly pathogenic forms of the human virus has highlighted the urgent need for new effective treatments. No current medication targets this heterotrimeric polymerase complex. All three subunits, PB1, PB2, and PA are required for both transcription and replication. PB1 carries the polymerase active site, PB2 includes the capped-RNA recognition domain, and PA is involved in assembly of the functional complex, but so far very little structural information has been reported for any of them. We describe the crystal structure of a large fragment of one subunit(PA)of influenza A RNA polymerase bound to a fragment of another subunit(PB1). The C terminal domain of PA forms a novel fold, and forms a deep, highly hydrophobic groove into which the N-terminal residues of PB1 can fit by forming a 310 helix.


J. Cryst. Soc. Jpn., 50(6), 335-340 (2008).
Solid State Photo-Reaction and Transformation of 5-Methyl-2-PyridoneCo-crystals Investigated by Ab Initio Powder X-ray Diffraction analysis
Kotaro FUJII1 and Hidehiro UEKUSA2
Affilication: 1, 2Department of Chemistry and Materials Science, Graduate School of Science and Engineering, Tokyo Institute of Technology
Address: 1, 22-12-1 Ookayama, Meguro, Tokyo 152-8551, Japan
E-Mail: 1kfujii(%)chem.titech.ac.jp, 2uekusa(%)cms.titech.ac.jp

Crystal A which is methanol solvate co-crystal of 5-methyl-2-pyridone(5MP)and trimesic acid(TMA)was found to transform to crystal B by grinding at atmosphere and both crystal A and B are found to transform to crystal C by heating. Interestingly, although crystal A and crystal B are not photo-reactive phase of pyridone, crystal C is photo-reactive and gave a pure[4+4]cis-syn pyridone dimer. In order to reveal the transformation mechanisms and the photo-reactivity, crystal structures of crystal B and crystal C were analyzed from X-ray powder diffraction data. The structural analyses revealed that crystal B is a hydrate co-crystal and crystal C is an unsolvated co-crystal. From the crystal structures, the photo-reactivity of these phases can be clearly explained by the reaction cavities of pyridone molecules in their crystals. These structural analyses also revealed that the transformation from crystal A to B is a solvent exchange process and crystal A or B to C is a desolvation process. Further, vapor induced transformations have been investigated for crystal A, B and C to establish the transformation mechanisms from the crystal structures point of view.


J. Cryst. Soc. Jpn., 50(6), 341-347 (2008).
Molecular Mechanism of the Redox-dependent Interaction betweenNADH-dependent Ferredoxin Reductase and Rieske-type Ferredoxin Miki SENDA, Shigenobu KIMURA, Masao FUKUDA,
Miki SENDA1 , Shigenobu KIMURA2 , Masao FUKUDA3 , Tetsuo ISHIDA4 and Toshiya SENDA5
Affilication: 1Japan Biological Informatics Consortium(JBIC), 2Department of Biomolecular Functional Engineering, Faculty of Engineering, Ibaraki University, 3Department of BioEngineering, Nagaoka University of Technology, 4Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, 5Biomedicinal Information Research Center(BIRC), National Institute of Advanced Industrial Science and Technology(AIST)
Address: 12-42 Aomi, Koto-ku, Tokyo 135-0064, Japan, 24-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan, 31603-1 Kamitomioka-cho, Nagaoka, Niigata 940-2188, Japan, 4Seta, Ohtsu, Shiga 520-2192, Japan, 52-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
E-Mail: 1miki-senda(%)aist.go.jp, 2s-kimura(%)mx.ibaraki.ac.jp, 3masao(%)vos.nagaokaut.ac.jp, 4teishida(%)belle.shiga-med.ac.jp, 5toshiya-senda(%)aist.go.jp

Redox-dependent affinity regulation is critical to fast and efficient electron transfer(ET)between ET proteins. The molecular mechanism of the affinity regulation, however, remains elusive due to the lack of crystal structures of the ET proteins in every redox state relevant to the ET reaction. BphA4 and BphA3 are, respectively, an FAD-containing NADH-dependent ferredoxin reductase and a Rieske-type[2Fe-2S]ferredoxin of a biphenyl dioxygenase BphA derived from Acidovorax sp. strain KKS102. Our biochemical study showed that the reduction of the FAD in BphA4 increases the affinity between BphA3 and BphA4 approximately 20-fold. In order to reveal the molecular mechanism of this redox-dependent affinity regulation, we determined the crystal structure of the following molecular species: BphA4 in oxidized, hydroquinone, semiquinone, and reoxidized forms; BphA3 in oxidized and reduced forms; and the ET complex of BphA3 and BphA4. A comparative analysis of these seven crystal structures obtained revealed that a series of conformational changes of BphA4 occurs upon reduction of FAD to form a high-affinity BphA3-binding site in BphA4.


J. Cryst. Soc. Jpn., 50(6), 348-353 (2008).
a Dithionite Group and Its Reaction Dynamics
Hidetaka NAKAI1 and Kiyoshi ISOBE2
Affilication: 1, 2Graduate School of Natural Science & Technology, Kanazawa University
Address: 1, 2Kakuma-machi, Kanazawa 920-1192
E-Mail: 1nakai(%)cacheibm.s.kanazawa-u.ac.jp, 2isobe(%)cacheibm.s.kanazawa-u.ac.jp

The compounds that undergo photochromic reaction in the crystalline-state are rare and their reaction dynamics are not well characterized as a result of the low degree of interconversion ratios and/or instability of the photo-generated isomers in the solid phase. We have recently found that a rhodium dinuclear complex[(RhCp*)2(m-CH2)2(m-O2SSO2)](Cp*=h5-C5Me5)having a photo-responsive dithionite group(m-O2SSO2)undergoes an essentially 100% reversible crystalline-state photochromism upon interconversion to[(RhCp*)2(m-CH2)2(m-O2SOSO)]. Taking an advantage of this unique full reversibility, we have investigated the dynamics of the system by using stepwise single crystal diffraction and variable-temperature solid-state NMR technique. The stereospecific oxygen-atom rearrangement process of the dithionite ligand and reorientational motion of the Cp* ligands, which are coupled to the photochromism, are presented.


J. Cryst. Soc. Jpn., 50(6), 354-358 (2008).
Time-Resolved X-ray Structural Investigation forAmorphous-Crystal Phase Change Process of DVD Optical Memory Materials
Shigeru KIMURA1 and Yoshihito TANAKA2
Affilication: 1Research & Utilization Division, Japan Synchrotron Radiation Research Institute, 2RIKEN SPring-8 Center
Address: 11-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo 679-5198, Japan, 21-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo 679-5148, Japan
E-Mail: 1kimuras(%)spring8.or.jp, 2yotanaka(%)riken.jp

A time-resolved structural investigation of the data storage process in a digital versatile disk(DVD)media has been desired for better understanding of the fast phase-change mechanism to get a clue in designing of higher performance optical recording material. Thus, the development of an in situ structural observation technique in the level of picosecond has been carried out for the investigation of the fast phase-change phenomena, by using synchrotron radiation pulsed X-rays and synchronized femtosecond laser irradiation. Then, for Ge2Sb2Te5 and Ag3.5In3.8Sb75.0Te17.7, the technique has been applied to a snapshot of X-ray diffraction observation of nanosecond crystallization process from amorphous to crystal phase which corresponds to erasing process of DVD recording system. The details of the time-resolved X-ray diffraction apparatus coupled with in situ photoreflectivity measurement and its performance are described.


J. Cryst. Soc. Jpn., 50(6), 359-364 (2008).
Recent Advances in the Crystallographic Study ofRhodopsin and Other G Protein-coupled Receptors
Tetsuji OKADA
Affiliation: Institute for Biomolecular Science, Gakushuin University
Address: 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
E-Mail: tetsuji.okada(%)gakushuin.ac.jp

Most eukaryotic organisms sense a majority of extracellular signals such as light, odorants and neurotransmitters via heptahelical membrane receptors called GPCRs, which are structurally distinct from microbial retinal proteins(photoreceptors). After several years from the first high-resolution structure determination of a prototypical GPCR visual rhodopsin in its inactive state, there has been significant progress over the past few years in the X-ray crystallographic study on this large family of receptors. Although the number of available structure is still limited, some valuable insights are obtained with regard to the structure and function of rhodopsin-like GPCRs.


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