A triclinic crystal form of Escherichia coli 4-diphosphocytidyl-2C-methyl-D-erythritol kinase and reassessment of the quaternary structure

Justyna Kalinowska-Tluscik, Linda Miallau, Mads Gabrielsen, Gordon A. Leonard, Sean M. McSweeney, William N. Hunter

    Research output: Contribution to journalArticle

    7 Citations (Scopus)

    Abstract

    4-Diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE; EC 2.7.1.148) contributes to the 1-deoxy-d-xylulose5-phosphate or mevalonate-independent bio-synthetic pathway that produces the isomers isopentenyl diphosphate and dimethylallyl diphosphate. These five-carbon compounds are the fundamental building blocks for the biosynthesis of isoprenoids. The mevalonate-independent pathway does not occur in humans, but is present and has been shown to be essential in many dangerous pathogens, i.e. Plasmodium species, which cause malaria, and Gram-negative bacteria. Thus, the enzymes involved in this pathway have attracted attention as potential drug targets. IspE produces 4-diphosphosphocytidyl-2C-methyl-d-erythritol 2-phosphate by ATP-dependent phosphorylation of 4-diphosphocytidyl-2C-methyl-d-erythritol. A triclinic crystal structure of the Escherichia coli IspE-ADP complex with two molecules in the asymmetric unit was determined at 2 angstrom resolution and compared with a monoclinic crystal form of a ternary complex of E. coli IspE also with two molecules in the asymmetric unit. The molecular packing is different in the two forms. In the asymmetric unit of the triclinic crystal form the substrate-binding sites of IspE are occluded by structural elements of the partner, suggesting that the 'triclinic dimer' is an artefact of the crystal lattice. The surface area of interaction in the triclinic form is almost double that observed in the monoclinic form, implying that the dimeric assembly in the monoclinic form may also be an artifact of crystallization.

    Original languageEnglish
    Pages (from-to)237-241
    Number of pages5
    JournalActa Crystallographica F-Structural Biology and Crystallization Communications
    Volume66
    DOIs
    Publication statusPublished - Mar 2010

    Keywords

    • NON-MEVALONATE PATHWAY
    • ISOPRENOID PRECURSOR BIOSYNTHESIS
    • TRYPANOSOMA-BRUCEI
    • DRUG DISCOVERY
    • ULTRACENTRIFUGATION
    • RECOGNITION
    • REFINEMENT
    • REACTIVITY
    • INHIBITORS
    • SYNTHASE

    Cite this

    @article{bf4d664103744d278a2bd4f2a9da0361,
    title = "A triclinic crystal form of Escherichia coli 4-diphosphocytidyl-2C-methyl-D-erythritol kinase and reassessment of the quaternary structure",
    abstract = "4-Diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE; EC 2.7.1.148) contributes to the 1-deoxy-d-xylulose5-phosphate or mevalonate-independent bio-synthetic pathway that produces the isomers isopentenyl diphosphate and dimethylallyl diphosphate. These five-carbon compounds are the fundamental building blocks for the biosynthesis of isoprenoids. The mevalonate-independent pathway does not occur in humans, but is present and has been shown to be essential in many dangerous pathogens, i.e. Plasmodium species, which cause malaria, and Gram-negative bacteria. Thus, the enzymes involved in this pathway have attracted attention as potential drug targets. IspE produces 4-diphosphosphocytidyl-2C-methyl-d-erythritol 2-phosphate by ATP-dependent phosphorylation of 4-diphosphocytidyl-2C-methyl-d-erythritol. A triclinic crystal structure of the Escherichia coli IspE-ADP complex with two molecules in the asymmetric unit was determined at 2 angstrom resolution and compared with a monoclinic crystal form of a ternary complex of E. coli IspE also with two molecules in the asymmetric unit. The molecular packing is different in the two forms. In the asymmetric unit of the triclinic crystal form the substrate-binding sites of IspE are occluded by structural elements of the partner, suggesting that the 'triclinic dimer' is an artefact of the crystal lattice. The surface area of interaction in the triclinic form is almost double that observed in the monoclinic form, implying that the dimeric assembly in the monoclinic form may also be an artifact of crystallization.",
    keywords = "NON-MEVALONATE PATHWAY, ISOPRENOID PRECURSOR BIOSYNTHESIS, TRYPANOSOMA-BRUCEI, DRUG DISCOVERY, ULTRACENTRIFUGATION, RECOGNITION, REFINEMENT, REACTIVITY, INHIBITORS, SYNTHASE",
    author = "Justyna Kalinowska-Tluscik and Linda Miallau and Mads Gabrielsen and Leonard, {Gordon A.} and McSweeney, {Sean M.} and Hunter, {William N.}",
    year = "2010",
    month = "3",
    doi = "10.1107/S1744309109054591",
    language = "English",
    volume = "66",
    pages = "237--241",
    journal = "Acta Crystallographica F-Structural Biology and Crystallization Communications",
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    publisher = "International Union of Crystallography",

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    A triclinic crystal form of Escherichia coli 4-diphosphocytidyl-2C-methyl-D-erythritol kinase and reassessment of the quaternary structure. / Kalinowska-Tluscik, Justyna; Miallau, Linda; Gabrielsen, Mads; Leonard, Gordon A.; McSweeney, Sean M.; Hunter, William N.

    In: Acta Crystallographica F-Structural Biology and Crystallization Communications, Vol. 66, 03.2010, p. 237-241.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - A triclinic crystal form of Escherichia coli 4-diphosphocytidyl-2C-methyl-D-erythritol kinase and reassessment of the quaternary structure

    AU - Kalinowska-Tluscik, Justyna

    AU - Miallau, Linda

    AU - Gabrielsen, Mads

    AU - Leonard, Gordon A.

    AU - McSweeney, Sean M.

    AU - Hunter, William N.

    PY - 2010/3

    Y1 - 2010/3

    N2 - 4-Diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE; EC 2.7.1.148) contributes to the 1-deoxy-d-xylulose5-phosphate or mevalonate-independent bio-synthetic pathway that produces the isomers isopentenyl diphosphate and dimethylallyl diphosphate. These five-carbon compounds are the fundamental building blocks for the biosynthesis of isoprenoids. The mevalonate-independent pathway does not occur in humans, but is present and has been shown to be essential in many dangerous pathogens, i.e. Plasmodium species, which cause malaria, and Gram-negative bacteria. Thus, the enzymes involved in this pathway have attracted attention as potential drug targets. IspE produces 4-diphosphosphocytidyl-2C-methyl-d-erythritol 2-phosphate by ATP-dependent phosphorylation of 4-diphosphocytidyl-2C-methyl-d-erythritol. A triclinic crystal structure of the Escherichia coli IspE-ADP complex with two molecules in the asymmetric unit was determined at 2 angstrom resolution and compared with a monoclinic crystal form of a ternary complex of E. coli IspE also with two molecules in the asymmetric unit. The molecular packing is different in the two forms. In the asymmetric unit of the triclinic crystal form the substrate-binding sites of IspE are occluded by structural elements of the partner, suggesting that the 'triclinic dimer' is an artefact of the crystal lattice. The surface area of interaction in the triclinic form is almost double that observed in the monoclinic form, implying that the dimeric assembly in the monoclinic form may also be an artifact of crystallization.

    AB - 4-Diphosphocytidyl-2C-methyl-d-erythritol kinase (IspE; EC 2.7.1.148) contributes to the 1-deoxy-d-xylulose5-phosphate or mevalonate-independent bio-synthetic pathway that produces the isomers isopentenyl diphosphate and dimethylallyl diphosphate. These five-carbon compounds are the fundamental building blocks for the biosynthesis of isoprenoids. The mevalonate-independent pathway does not occur in humans, but is present and has been shown to be essential in many dangerous pathogens, i.e. Plasmodium species, which cause malaria, and Gram-negative bacteria. Thus, the enzymes involved in this pathway have attracted attention as potential drug targets. IspE produces 4-diphosphosphocytidyl-2C-methyl-d-erythritol 2-phosphate by ATP-dependent phosphorylation of 4-diphosphocytidyl-2C-methyl-d-erythritol. A triclinic crystal structure of the Escherichia coli IspE-ADP complex with two molecules in the asymmetric unit was determined at 2 angstrom resolution and compared with a monoclinic crystal form of a ternary complex of E. coli IspE also with two molecules in the asymmetric unit. The molecular packing is different in the two forms. In the asymmetric unit of the triclinic crystal form the substrate-binding sites of IspE are occluded by structural elements of the partner, suggesting that the 'triclinic dimer' is an artefact of the crystal lattice. The surface area of interaction in the triclinic form is almost double that observed in the monoclinic form, implying that the dimeric assembly in the monoclinic form may also be an artifact of crystallization.

    KW - NON-MEVALONATE PATHWAY

    KW - ISOPRENOID PRECURSOR BIOSYNTHESIS

    KW - TRYPANOSOMA-BRUCEI

    KW - DRUG DISCOVERY

    KW - ULTRACENTRIFUGATION

    KW - RECOGNITION

    KW - REFINEMENT

    KW - REACTIVITY

    KW - INHIBITORS

    KW - SYNTHASE

    U2 - 10.1107/S1744309109054591

    DO - 10.1107/S1744309109054591

    M3 - Article

    VL - 66

    SP - 237

    EP - 241

    JO - Acta Crystallographica F-Structural Biology and Crystallization Communications

    JF - Acta Crystallographica F-Structural Biology and Crystallization Communications

    SN - 1744-3091

    ER -