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Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis

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ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2003年第1期59卷 23-31页

作者： Kishida, H Wada, T Unzai, S Kuzuyama, T Takagi, M Terada, T Shirouzu, M Yokoyama, S Tame, JRH Park, SY Yokohama City Univ Grad Sch Integrated Sci Prot Design Lab Yokohama Kanagawa 2300045 Japan RIKEN Yokohama Inst Genom Sci Ctr Yokohama Kanagawa 2300045 Japan Univ Tokyo Inst Mol & Cellular Biosci Bunkyo Ku Tokyo 1130032 Japan RIKEN Harima Inst SPring 8 Sayo Hyogo 6795148 Japan Univ Tokyo Grad Sch Sci Dept Biophys & Biochem Bunkyo Ku Tokyo 1130033 Japan

Precursors for isoprenoid synthesis are essential in all organisms. These compounds are synthesized by one of two known routes: the well characterized mevalonate pathway or a recently discovered non-mevalonate route which is used in many bacteria and human pathogens. Since the second pathway is both vital and unlike any found in humans, enzymes catalysing reactions along this synthetic route are possible drug targets. The structure of one such enzyme from the thermophilic bacterium Thermus thermophilus has been solved to high resolution in the presence of substrate and with a substrate analogue. Enzyme co-crystallized with substrate shows only one product, cytosine monophosphate (CMP), in the active site. At the high resolution of the refinement (1.6 Angstrom) the positions and coordination of the magnesium ions in the active site are clearly seen.

关键词：氨基酸序列细菌蛋白质类/化学细菌蛋白质类/遗传学细菌蛋白质类/分离和提纯细菌蛋白质类/代谢结合部位催化作用结晶学 X线胞苷一磷酸/代谢大肠杆菌蛋白质类赖氨酸/代谢镁/化学镁/代谢甲羟戊酸/代谢模型分子分子序列数据磷氧裂合酶类/化学磷氧裂合酶类/遗传学磷氧裂合酶类/分离和提纯磷氧裂合酶类/代谢聚异戊烯磷酸盐类/生物合成蛋白质构象重组蛋白质类/化学重组蛋白质类/遗传学重组蛋白质类/分离和提纯重组蛋白质类/代谢序列同源性氨基酸底物特异性嗜热栖热菌属/酶学

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Crystallization and preliminary X-ray analysis of Yersinia pseudotuberculosis-derived mitogen

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ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2003年第7期59卷 1330-1332页

作者： Donadini, R Wåhlberga, M Kohsaka, T Ito, Y Fields, BA Univ Sydney Sch Mol & Microbial Biosci Sydney NSW 2006 Australia Natl Childrens Med Res Ctr Dept Allergy & Immunol Setagaya Ku Tokyo 1548509 Japan

Yersinia pseudotuberculosis-derived mitogen (YPM), a superantigen with no amino-acid sequence similarity to other known superantigens, has been crystallized by the sitting-drop vapour-diffusion method. The crystals belong to space group C2, with unit-cell parameters a = 138.67, b = 78.66, c = 32.91 Angstrom, beta = 91.97degrees. A native data set has been collected to a resolution of 1.8 Angstrom using synchrotron radiation. Self-rotation function calculations suggest the presence of three molecules in the asymmetric unit, corresponding to a solvent content of 45%.

关键词：细菌蛋白质类/化学细菌蛋白质类/遗传学细菌蛋白质类/分离和提纯克隆分子结晶大肠杆菌/遗传学有丝分裂原/化学重组融合蛋白质类硒代甲硫氨酸超抗原/化学 X线衍射假结核病耶尔森菌/化学

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Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of the F1 antigen Caf1M-Caf1 chaperone-subunit pre-assembly complex from Yersinia pestis

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ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2003年第2期59卷 359-362页

作者： Zavialov, A Berglund, J Knight, SD Swedish Univ Agr Sci Uppsala Biomed Ctr Dept Biol Mol SE-75324 Uppsala Sweden

The F1 capsular antigen of the plague-causing pathogen Yersinia pestis is assembled from monomeric Caf1 subunits via the Caf1M/Caf1A chaperone/usher system. Y. pestis Caf1M-Caf1 chaperone-subunit complex was purified from the periplasm of Escherichia coli cells overexpressing Caf1M and Caf1 and was crystallized in PEG 4000 solution using hanging-drop vapour diffusion. The crystals diffract to a minimum Bragg spacing of 1.8 Angstrom and belong to space group P2(1), with unit-cell parameters a = 36.0, b = 69.2, c = 69.1 Angstrom, beta = 93.0degrees. SeMet-labelled Caf1M-Caf1 complexes were purified and crystallized under the same conditions. The SeMet crystals were identical to the native crystals and diffracted to 1.9 Angstrom. Heavy-atom derivative crystals were prepared by soaking in 10 mM K2PtCl4, giving two Pt sites per complex. The experimental electron-density map was obtained by a combination of MAD and MIR methods using both Se- and Pt-derivative crystals.

关键词：抗原细菌/生物合成抗原细菌/化学抗原细菌/遗传学抗原细菌/分离和提纯细菌蛋白质类/生物合成细菌蛋白质类/化学细菌蛋白质类/遗传学细菌蛋白质类/分离和提纯结晶/方法结晶学 X线/方法大肠杆菌/遗传学大肠杆菌/代谢分子伴侣/化学分子伴侣/遗传学蛋白质亚单位/化学重组融合蛋白质类/生物合成重组融合蛋白质类/化学重组融合蛋白质类/遗传学重组融合蛋白质类/分离和提纯静电学鼠疫耶尔森菌/化学鼠疫耶尔森菌/遗传学

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Biotechnologically relevant enzymes from Thermus thermophilus

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APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 2002年第1期58卷 1-12页

作者： Pantazaki, AA Pritsa, AA Kyriakidis, DA Aristotelian Univ Thessaloniki Dept Chem Biochem Lab GR-54006 Thessaloniki Greece

Enzymes produced by Thermus thermophilus are of considerable biotechnological interest. This review covers industrial applications of several protein products of this thermophilic bacterium that are functional under extreme conditions. The purification of proteins from T. thermophilus using either conventional methods or in the light of the cloning of their genes and expression in mesophilic microorganisms is discussed. Enzymes that biodegrade proteins, polysaccharides or key enzymes that are involved in amino acid metabolism, protein folding or in other fundamental biological processes such as DNA replication, DNA repair, and RNA maturation, with potential use in different biotechnological processes are reviewed as well.

关键词：细菌蛋白质类/遗传学细菌蛋白质类/分离和提纯细菌蛋白质类/代谢生物技术/方法酶类/遗传学酶类/分离和提纯酶类/代谢栖热菌属嗜热/酶学栖热菌属嗜热/遗传学

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Cyclic lipoundecapeptide amphisin from Pseudomonas sp strain DSS73

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ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2001年第9期57卷 1123-1124页

作者： Sorensen, D Nielsen, TH Christophersen, C Sorensen, J Gajhede, M Univ Copenhagen Dept Chem Prot Struct Grp DK-2100 Copenhagen Denmark Univ Copenhagen Dept Chem Marine Chem Sect DK-2100 Copenhagen Denmark Royal Vet & Agr Univ Dept Ecol Sect Genet & Microbiol DK-1871 Copenhagen C Denmark

The crystal structure of the lipoundecapeptide amphisin, presented here as the tetrahydrate, C66H114N12O20. 4H(2)O, originating from non-ribosomal biosynthesis by Pseudomonas sp. strain DSS73, has been solved to a resolution of 0.65 Angstrom. The primary structure of amphisin is beta -hydroxydecanoyld-Leu-D-Asp-D-allo-Thr-D-Leu-D-Leu-D-Ser-L-Leu-D-Gln-L- Leu-l-Ile-l-Asp (Leu is leucine, Asp is aspartic acid, Thr is threonine, Ser is serine, Gln is glutamine and Ile is isoleucine). The peptide is a lactone, linking Thr4 O-gamma to the C-terminal. The stereochemistry of the beta -hydroxy acid is R. The peptide is a close analogue of the cyclic lipopeptides tensin and pholipeptin produced by Pseudomonas fluorescens. The structure of amphisin is mainly helical (3(10)-helix), with the cyclic peptide wrapping around a hydrogen-bonded water molecule. This lipopeptide is amphiphilic and has biosurfactant and antifungal properties.

关键词：细菌蛋白质类/化学细菌蛋白质类/分离和提纯结晶学 X线脂蛋白类/化学脂蛋白类/分离和提纯模型分子肽类环/化学肽类环/分离和提纯蛋白质构象假单胞菌属/化学假单胞菌属/代谢

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Crystallization of the Bacillus thuringiensis toxin Cry1Ac and its complex with the receptor ligand N-acetyl-D-galactosamine

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ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2001年第12期57卷 1938-1944页

作者： Derbyshire, DJ Ellar, DJ Li, J MRC Mol Biol Lab Cambridge CB2 2QH England Univ Cambridge Dept Biochem Cambridge CB2 1GA England

Cry1Ac from Bacillus thuringiensis ssp. kurstaki HD-73 is a pore-forming protein specifically toxic to lepidopteran insect larvae. It binds to the cell-surface receptor aminopeptidase N in Manduca sexta midgut via the sugar N-acetyl-D-galactosamine (GalNAc). By using 1,3-diaminopropane (DAP) as the buffer throughout protoxin activation and chromatography on Q-Sepharose at pH 10.3, trypsin-activated Cry1Ac has been purified in a monomeric state, which was crucial to obtaining single crystals of Cry1Ac and of the Cry1Ac-GalNAc complex. Crystals of Cry1Ac alone are triclinic, with unit-cell parameters a=51.78, b=113.23, c=123.41 Angstrom, alpha =113.11, beta =91.49, gamma =100.46 degrees;those of the Cry1Ac-GalNAc complex show P2(1) symmetry, with unit-cell parameters a=121.36, b=51.19, c=210.56 Angstrom, beta =105.75 degrees. Data sets collected to 2.36 and 2.95 Angstrom resolution, respectively, show that both crystal forms contain four molecules of the 66 kDa toxin in the asymmetric unit and have related packing arrangements. The deaggregating effect of DAP may be explained by its capacity for bivalent hydrogen bonding and hydrophobic interactions at protein interfaces.

关键词：乙酰半乳糖胺/化学苏云金芽孢杆菌/化学细菌蛋白质类/化学细菌蛋白质类/分离和提纯细菌毒素类结合部位结晶结晶学 X线内毒素类/化学内毒素类/分离和提纯溶血素蛋白质类微绒毛/代谢模型分子蛋白质构象

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Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance A (NusA) from Mycobacterium tuberculosis

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ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 2001年第8期57卷 1187-1188页

作者： Gopal, B Papavinasasundaram, KG Colston, MJ Dodson, G Haire, LF Natl Inst Med Res Div Prot Struct London NW7 1AA England Natl Inst Med Res Div Mycobacterial Res London NW7 1AA England

N-utilizing substance A (NusA) is a protein which performs several roles as a cofactor of DNA-dependent RNA polymerase. Its acts as an elongation factor and facilitates pausing, termination and the formation of a complex assembly that mediates transcription antitermination in eubacteria. Biochemical and biophysical data in the literature suggest that this protein performs these functions by binding to the core RNA polymerase, other protein factors and certain RNA fragments having specific signal sequences. The NusA of Mycobacterium tuberculosis has been cloned and overexpressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. The space group is P3(1)21, with unit-cell parameters a = b = 78.1, c = 180.3 Angstrom. A native data set complete to 1.7 Angstrom resolution has been collected from a single crystal.

关键词：细菌蛋白质类/生物合成细菌蛋白质类/化学细菌蛋白质类/分离和提纯克隆分子结晶结晶学 X线大肠杆菌蛋白质类结核分枝杆菌/化学肽延伸因子蛋白质构象转录因子/生物合成转录因子/化学转录因子/分离和提纯转录延伸因子类

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Cloning, purification, crystallization and preliminary crystallographic analysis of Bacillus subtilis LuxS

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ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2001年第9期57卷 1324-1325页

作者： Das, SK Sedelnikova, SE Baker, PJ Ruzheinikov, SN Foster, S Hartley, A Horsburgh, MJ Rice, DW Univ Sheffield Krebs Inst Biomolec Res Dept Mol Biol & Biotechnol Sheffield S10 2TN S Yorkshire England

LuxS of Bacillus subtilis is a member of a novel family of proteins with a potential role in quorum sensing, controlling important aspects of cellular physiology in a range of microbial species. B. subtilis luxS was cloned, expressed in Escherichia coli, purified and crystallized using the hanging-drop method of vapour diffusion with ammonium sulfate as the precipitant. The crystals belong to one of the enantiomorphic space groups P6(1)22 or P6(5)22, with approximate unit-cell parameters a = b = 63.6, c = 151.5 Angstrom and one subunit in the asymmetric unit, corresponding to a packing density of 2.5 Angstrom (3) Da(-1). The crystals diffract X-rays to at least 1.55 Angstrom resolution on a synchrotron-radiation source. Determination of the structure will provide insights into the key determinants of function of this class of proteins, for which no structures are currently available.

关键词：枯草芽孢杆菌/化学细菌蛋白质类/化学细菌蛋白质类/遗传学细菌蛋白质类/分离和提纯碳硫裂合酶类克隆分子结晶结晶学 X线蛋白质构象重组蛋白质类/化学重组蛋白质类/分离和提纯

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Isolation and characterization of a cell-associated protein of Bacillus pumilus PH-01

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APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 2001年第3-4期56卷 402-405页

作者： Hong, HB Chang, YS Choi, SD Nam, IH Lee, YE Pohang Univ Sci & Technol Sch Environm Engn Nam Gu Pohang 790784 South Korea Dongguk Univ Dept Biochem Kyungju 780714 South Korea

A cell-associated protein released from Bacillus pumilus PH-01 showed an affinity for some dioxins, like 1,2,3,4-tetrachlorodibenzo-p-dioxin (TCDD) and 1,2,3,4-tetrachlorodibenzofuran (TCDF), and the concentration of the protein increased when B. pumilus PH-01 was boiled in minimal salts medium. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization-mass spectrometry revealed that the boiled culture supernatant contained a major protein with a molecular mass of 5,313.4 Da. The adsorption behavior of the protein for 1,2,3,4-TCDD and 1,2,3,4-TCDF was examined by digesting it with proteinase K and trypsin, showing that the proteolyzed protein lost the ability to adsorb the compounds. The amino acid sequence of the protein was determined by automated Edman degradation and tandem mass spectrometry. A search of the protein databases showed no existence of proteins with an homologous sequence.

关键词：吸附氨基酸序列芽孢杆菌属/生长和发育芽孢杆菌属/代谢细菌蛋白质类/化学细菌蛋白质类/分离和提纯细菌蛋白质类/代谢苯呋喃类/化学苯呋喃类/药代动力学二恶辛类/药代动力学四氯二苯并二恶英/药代动力学

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Temperature dependence of DNA affinity chromatography of transcription factors

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ANALYTICAL BIOCHEMISTRY 2000年第2期279卷 209-217页

作者： Jarrett, HW Univ Tennessee Dept Biochem Memphis TN 38163 USA

Oligonucleotides bound by the CAAT enhancer binding protein (C/EBP), the lactose repressor, and Gal4 were chemically coupled to cyanogen bromide-activated Sepharose and the temperature dependence of transcription factor chromatography was characterized, Each transcription factor was applied to the ap appropriate column and eluted using a salt gradient at several temperatures, Each transcription factor showed a unique behavior. As temperature was increases, less salt was required to elute C/EBP, more salt was required to elute lac repressor, while Gal4 showed a biphasic dependency with the amount of salt first decreasing between 4 and 19 degrees C and then increasing above 19 degrees C. This temperature dependence is not due to protein or DNA unfolding but rather is a property of complex formation. By loading a column, washing it at a permissive temperature, and then rapidly changing the column temperature, highly selective elution can be obtained. The thermodynamics of this temperature effect are different for the binding of specific and nonspecific DNA sequences, making chromatography at different temperatures a potentially important way of purifying transcription factors, (C) 2000 Academic Press.

关键词：细菌蛋白质类/分离和提纯碱基序列 CCAAT增强子结合蛋白类色谱法亲和/方法 DNA/遗传学 DNA引物/遗传学 DNA结合蛋白质类/分离和提纯静电学大肠杆菌蛋白质类评价研究真菌蛋白质类/分离和提纯绿色荧光蛋白质类发光蛋白质类/分离和提纯核蛋白质类/分离和提纯蛋白质结合重组融合蛋白质类/分离和提纯阻遏蛋白质类/分离和提纯酿酒酵母蛋白质类温度热力学转录因子/分离和提纯

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