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2005～2007年の研究業績

2005年から2007年までに当研究室が論文として発表した研究業績の一覧です。

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2007年

  • A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed β-propeller
  • Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, Hashimoto W, Murata K
  • J Biol Chem. 2007 Dec 21;282(51):37134-37145. Epub 2007 Oct 17.  » [Pubmed]
  • Crystal structure of glycoside hydrolase family 78 α-L-Rhamnosidase from Bacillus sp. GL1
  • Cui Z, Maruyama Y, Mikami B, Hashimoto W, Murata K
  • J Mol Biol. 2007 Nov 23;374(2):384-398. Epub 2007 Sep 8.  » [Pubmed]
  • Specific and high-affinity binding of tetramerized PD-L1 extracellular domain to PD-1-expressing cells: possible application to enhance T cell function
  • Terawaki S, Tanaka Y, Nagakura T, Hayashi T, Shibayama S, Muroi K, Okazaki T, Mikami B, Garboczi DN, Honjo T, Minato N
  • Int Immunol. 2007 Jul;19(7):881-890. Epub 2007 Jul 2.  » [Pubmed]
  • Preliminary crystallographic analysis of L-2-keto-3-deoxyarabonate dehydratase, an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism
  • Shimada N, Mikami B, Watanabe S, Makino K
  • Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 May 1;63(Pt 5):393-395. Epub 2007 Apr 6.  » [Pubmed]
  • A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan
  • Maruyama Y, Mikami B, Hashimoto W, Murata K
  • Biochemistry. 2007 Jan 23;46(3):781-791.  » [Pubmed]
  • Synthesis of pyrophosphate-containing compounds that stimulate Vγ2Vδ2 T cells: application to cancer immunotherapy
  • Tanaka Y, Kobayashi H, Terasaki T, Toma H, Aruga A, Uchiyama T, Mizutani K, Mikami B, Morita CT, Minato N
  • Med Chem. 2007 Jan;3(1):85-99.  » [Pubmed]
  • [Review] Hydration of vinyl ether groups by unsaturated glycoside hydrolases and their role in bacterial pathogenesis
  • Hashimoto W, Itoh T, Maruyama Y, Mikami B, Murata K
  • Int Microbiol. 2007 Dec;10(4):233-243.  » [Pubmed]

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2006年

  • Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism
  • Itoh T, Hashimoto W, Mikami B, Murata K
  • J Biol Chem. 2006 Oct 6;281(40):29807-29816. Epub 2006 Aug 7.  » [Pubmed]
  • Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate
  • Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K
  • Biochem Biophys Res Commun. 2006 Sep 8;347(4):1021-1029. Epub 2006 Jul 17.  » [Pubmed]
  • Thermostabilization of ovotransferrin by anions for pasteurization of liquid egg white
  • Mizutani K, Chen Y, Yamashita H, Hirose M, Aibara S
  • Biosci Biotechnol Biochem. 2006 Aug;70(8):1839-1845.  » [Pubmed]
  • Structure of 8Sα globulin, the major seed storage protein of mung bean
  • Itoh T, Garcia RN, Adachi M, Maruyama Y, Tecson-Mendoza EM, Mikami B, Utsumi S
  • Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):824-832. Epub 2006 Jun 20.  » [Pubmed]
  • Sequence and analysis of the 46.6-kb plasmid pA1 from Sphingomonas sp. A1 that corresponds to the typical IncP-1β plasmid backbone without any accessory gene
  • Harada KM, Aso Y, Hashimoto W, Mikami B, Murata K
  • Plasmid. 2006 Jul;56(1):11-23. Epub 2006 Jan 30.  » [Pubmed]
  • A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide
  • Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K
  • J Mol Biol. 2006 Jul 14;360(3):573-585. Epub 2006 May 9.  » [Pubmed]
  • Crystallization and preliminary crystallographic analysis of the family GH78 α-L-rhamnosidase RhaB from Bacillus sp. GL1
  • Cui Z, Maruyama Y, Mikami B, Hashimoto W, Murata K
  • Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Jul 1;62(Pt 7):646-648. Epub 2006 Jun 10.  » [Pubmed]
  • Crystal structure of pullulanase: evidence for parallel binding of oligosaccharides in the active site
  • Mikami B, Iwamoto H, Malle D, Yoon HJ, Demirkan-Sarikaya E, Mezaki Y, Katsuya Y
  • J Mol Biol. 2006 Jun 9;359(3):690-707. Epub 2006 Apr 18.  » [Pubmed]
  • Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1
  • Itoh T, Hashimoto W, Mikami B, Murata K
  • Biochem Biophys Res Commun. 2006 May 26;344(1):253-262.  » [Pubmed]
  • Crystallization and preliminary X-ray analysis of an exotype alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, a member of polysaccharide lyase family 15
  • Ochiai A, Yamasaki M, Mikami B, Hashimoto W, Murata K
  • Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 May 1;62(Pt 5):486-488. Epub 2006 Apr 28.  » [Pubmed]
  • Crystallization and preliminary X-ray analysis of the rhamnogalacturonan lyase YesW from Bacillus subtilis strain 168, a member of polysaccharide lyase family 11
  • Ochiai A, Yamasaki M, Itoh T, Mikami B, Hashimoto W, Murata K
  • Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 May 1;62(Pt 5):438-440. Epub 2006 Apr 12.  » [Pubmed]
  • Overexpression, purification and preliminary X-ray analysis of pullulanase from Bacillus subtilis strain 168
  • Malle D, Itoh T, Hashimoto W, Murata K, Utsumi S, Mikami B
  • Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt 4):381-384. Epub 2006 Mar 25.  » [Pubmed]
  • Engineered membrane superchannel improves bioremediation potential of dioxin-degrading bacteria
  • Aso Y, Miyamoto Y, Harada KM, Momma K, Kawai S, Hashimoto W, Mikami B, Murata K
  • Nat Biotechnol. 2006 Feb;24(2):188-189. Epub 2006 Jan 15.  » [Pubmed]
  • Crystal structure of a metal ion-bound IS200 transposase
  • Lee HH, Yoon JY, Kim HS, Kang JY, Kim KH, Kim DJ, Ha JY, Mikami B, Yoon HJ, Suh SW
  • J Biol Chem. 2006 Feb 17;281(7):4261-4266. Epub 2005 Dec 11.  » [Pubmed]
  • Crystal structure and some properties of a major house dust mite allergen, Derf 2
  • Suzuki M, Tanaka Y, Korematsu S, Mikami B, Minato N
  • Biochem Biophys Res Commun. 2006 Jan 13;339(2):679-686. Epub 2005 Nov 21.  » [Pubmed]

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2005年

  • Structure of aluminium-bound ovotransferrin at 2.15 Å resolution
  • Mizutani K, Mikami B, Aibara S, Hirose M
  • Acta Crystallogr D Biol Crystallogr. 2005 Dec;61(Pt 12):1636-1642. Epub 2005 Nov 19.  » [Pubmed]
  • Proteomics-based identification of outer-membrane proteins responsible for import of macromolecules in Sphingomonas sp. A1: alginate-binding flagellin on the cell surface
  • Hashimoto W, He J, Wada Y, Nankai H, Mikami B, Murata K
  • Biochemistry. 2005 Oct 25;44(42):13783-13794.  » [Pubmed]
  • A structural basis for depolymerization of alginate by polysaccharide lyase family-7
  • Yamasaki M, Ogura K, Hashimoto W, Mikami B, Murata K
  • J Mol Biol. 2005 Sep 9;352(1):11-21.  » [Pubmed]
  • Overall carbohydrate-binding properties of Castanea crenata agglutinin (CCA)
  • Nomura K, Takahashi N, Hirose M, Nakamura S, Yagi F
  • Carbohydr Res. 2005 Sep 5;340(12):2004-2009.  » [Pubmed]
  • Structural basis of a fungal galectin from Agrocybe cylindracea for recognizing sialoconjugate
  • Ban M, Yoon HJ, Demirkan E, Utsumi S, Mikami B, Yagi F
  • J Mol Biol. 2005 Aug 26;351(4):695-706.  » [Pubmed]
  • Crystal structure of nicotinic acid mononucleotide adenylyltransferase from Pseudomonas aeruginosa in its Apo and substrate-complexed forms reveals a fully open conformation
  • Yoon HJ, Kim HL, Mikami B, Suh SW
  • J Mol Biol. 2005 Aug 12;351(2):258-265.  » [Pubmed]
  • Glycosylation of genistin into soluble inclusion complex form of cyclic glucans by enzymatic modification
  • Li D, Roh SA, Shim JH, Mikami B, Baik MY, Park CS, Park KH
  • J Agric Food Chem. 2005 Aug 10;53(16):6516-6524.  » [Pubmed]
  • Α-Amylase from B. amyloliquefaciens: purification, characterization, raw starch degradation and expression in E coli
  • Sarikaya-Demirkan E, Mikami B, Adachi M, Higasa T, Utsumi S
  • Process Biochem. 2005 Jul;40(8): 2629-2636.
  • Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: insights into the enzyme reaction mechanism
  • Maruyama Y, Hashimoto W, Mikami B, Murata K
  • J Mol Biol. 2005 Jul 29;350(5):974-986.  » [Pubmed]
  • Crystallization and preliminary X-ray crystallographic analysis of UDP-N-acetylglucosamine enolpyruvyl transferase from Haemophilus influenzae in complex with UDP-N-acetylglucosamine and fosfomycin
  • Yoon HJ, Ku MJ, Ahn HJ, Lee BI, Mikami B, Suh SW
  • Mol Cells. 2005 Jun 30;19(3):398-401.  » [Pubmed]
  • Molecular conversion of NAD kinase to NADH kinase through single amino acid residue substitution
  • Mori S, Kawai S, Shi F, Mikami B, Murata K
  • J Biol Chem. 2005 Jun 24;280(25):24104-24112. Epub 2005 Apr 26.  » [Pubmed]
  • Thermostability of refolded ovalbumin and S-ovalbumin
  • Takahashi N, Onda M, Hayashi K, Yamasaki M, Mita T, Hirose M
  • Biosci Biotechnol Biochem. 2005 May;69(5):922-931.  » [Pubmed]
  • Dynamic mechanism for the serpin loop insertion as revealed by quantitative kinetics
  • Takahashi N, Terakado K, Nakamura G, Soekmadji C, Masuoka T, Yamasaki M, Hirose M
  • J Mol Biol. 2005 Apr 29;348(2):409-418.  » [Pubmed]
  • Structural analysis of threonine 342 mutants of soybean β-amylase: role of a conformational change of the inner loop in the catalytic mechanism
  • Kang YN, Tanabe A, Adachi M, Utsumi S, Mikami B
  • Biochemistry. 2005 Apr 5;44(13):5106-5116.  » [Pubmed]
  • Direct evidence for Sphingomonas sp. A1 periplasmic proteins as macromolecule-binding proteins associated with the ABC transporter: molecular insights into alginate transport in the periplasm
  • Momma K, Mishima Y, Hashimoto W, Mikami B, Murata K
  • Biochemistry. 2005 Apr 5;44(13):5053-5064.  » [Pubmed]
  • Crystallization and preliminary X-ray analysis of alginate lyases A1-II and A1-II' from Sphingomonas sp. A1
  • Yamasaki M, Ogura K, Moriwaki S, Hashimoto W, Murata K, Mikami B
  • Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Mar 1;61(Pt 3):288-290. Epub 2005 Feb 12.  » [Pubmed]
  • Microstructures of bread dough and the effects of shortening on frozen dough
  • Aibara S, Ogawa N, Hirose M
  • Biosci Biotechnol Biochem. 2005 Feb;69(2):397-402.  » [Pubmed]
  • NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex
  • Mori S, Yamasaki M, Maruyama Y, Momma K, Kawai S, Hashimoto W, Mikami B, Murata K
  • Biochem Biophys Res Commun. 2005 Feb 11;327(2):500-508.  » [Pubmed]
  • Crystal structure of cold-active protein-tyrosine phosphatase from a psychrophile, Shewanella sp.
  • Tsuruta H, Mikami B, Aizono Y
  • J Biochem. 2005 Jan;137(1):69-77.  » [Pubmed]
  • Crystallization and preliminary crystallographic analysis of endo-1,3-β-glucanase from Arthrobacter sp.
  • Pang Z, Kang YN, Ban M, Oda M, Kobayashi R, Ohnishi M, Mikami B
  • Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jan 1;61(Pt 1):68-70. Epub 2004 Nov 9.  » [Pubmed]
  • [Review] Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules
  • Hashimoto W, Momma K, Maruyama Y, Yamasaki M, Mikami B, Murata K
  • Biosci Biotechnol Biochem. 2005 Apr;69(4):673-692.  » [Pubmed]
  • [Review] Hypothesis: structures, evolution, and ancestor of glucose kinases in the hexokinase family
  • Kawai S, Mukai T, Mori S, Mikami B, Murata K
  • J Biosci Bioeng. 2005 Apr;99(4):320-330.  » [Pubmed]
  • [Book] タンパク質の結晶化
  • 坂部知平監修, 相原茂夫編著
  • 京都大学学術出版会　pp.-445

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