Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids

Steinbacher, Stefan; Kaiser, J.; Wungsintaweekul, Juraithip; Hecht, Stefan; Eisenreich, Wolfgang; Gerhardt, S.; Bacher, Adelbert; Rohdich, Felix

doi:10.1006/jmbi.2001.5341

Cited by 76 publications

(112 citation statements)

References 34 publications

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“…Such chemical validation of the reductoisomerase is complemented by genetic studies, which have proven that the enzymes responsible for stages three to five of the pathway are essential in eubacteria (27)(28)(29)(30)(31). The crystallographic studies necessary to support structure-based drug discovery have produced models for DOXP reductoisomerase (32)(33)(34), 2C-methyl-D-erythritol-4-phosphate cytidylyltransferase (15,35), and 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (36)(37)(38)(39). We now turn our attention to CDP-ME kinase.…”

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confidence: 99%

Biosynthesis of isoprenoids: Crystal structure of 4-diphosphocytidyl-2C-methyl- d -erythritol kinase

Miallau

Alphey

Kemp

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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109

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4-Diphosphocytidyl-2C-methyl-D-erythritol kinase, an essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis, catalyzes the single ATP-dependent phosphorylation stage affording 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate. The 2-Å resolution crystal structure of the Escherichia coli enzyme in a ternary complex with substrate and a nonhydrolyzable ATP analogue reveals the molecular determinants of specificity and catalysis. The enzyme subunit displays the ␣͞␤ fold characteristic of the galactose kinase͞ homoserine kinase͞mevalonate kinase͞phosphomevalonate kinase superfamily, arranged into cofactor and substrate-binding domains with the catalytic center positioned in a deep cleft between domains. Comparisons with related members of this superfamily indicate that the core regions of each domain are conserved, whereas there are significant differences in the substrate-binding pockets. The nonmevalonate pathway is essential in many microbial pathogens and distinct from the mevalonate pathway used by mammals. The high degree of sequence conservation of the enzyme across bacterial species suggests similarities in structure, specificity, and mechanism. Our model therefore provides an accurate template to facilitate the structure-based design of broad-spectrum antimicrobial agents.galactose kinase͞homoserine kinase͞mevalonate kinase͞ phosphomevalonate kinase ͉ enzyme mechanism ͉ nonmevalonate ͉ phosphorylation T he AT P-dependent 4-diphosphocytidyl-2C-methyl-Derythritol (CDP-ME) kinase (EC 2.7.1.148) participates in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). These isomers are the universal five-carbon precursors of isoprenoids, a diverse and important family of natural products that includes sterols, dolichols, triterpenes, and ubiquinones, and components of macromolecules such as the prenyl groups of prenylated proteins and isopentenylated tRNAs (1-3). Isoprenoids contribute to many biological functions, including electron transport in respiration and photosynthesis, hormone-based signaling, apoptosis, meiosis, protein cleavage, and degradation (4). In addition, they provide important structural components of cell membranes (1).Two biosynthetic routes to IPP and DMAPP have evolved. In eukaryotes, archaebacteria, and a few eubacteria, the precursor biosynthesis is through the mevalonate pathway (3-7). This begins with the conversion of three molecules of acetyl-CoA to 3-hydroxy-3-methylglutaryl-CoA followed by reduction, phosphorylation, and decarboxylation to generate IPP, some of which is isomerized to DMAPP. The last three steps in this pathway are ATP-dependent and catalyzed by the structurally related mevalonate kinase (MVK), phosphomevalonate kinase, and mevalonate 5-diphosphate decarboxylase.In chloroplasts, algae, cyanobacteria, most eubacteria, and the apicomplexa, IPP and DMAPP synthesis is accomplished by seven enzymes in a pathway named after one of the intermediates, the 1-deoxy-D-xylulose-5-ph...

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mentioning

confidence: 99%

Biosynthesis of isoprenoids: Crystal structure of 4-diphosphocytidyl-2C-methyl- d -erythritol kinase

Miallau

Alphey

Kemp

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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109

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“…While this manuscript was under review, two lower-resolution structures of this enzyme were reported (47,48). There is good Fig.…”

Section: Resultsmentioning

confidence: 94%

Structure of 2C-methyl- d -erythritol 2,4- cyclodiphosphate synthase: An essential enzyme for isoprenoid biosynthesis and target for antimicrobial drug development

Kemp

Bond

Hunter

2002

Proc. Natl. Acad. Sci. U.S.A.

104

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The crystal structure of the zinc enzyme Escherichia coli 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase in complex with cytidine 5 -diphosphate and Mn 2؉ has been determined to 1.8-Å resolution. This enzyme is essential in E. coli and participates in the nonmevalonate pathway of isoprenoid biosynthesis, a critical pathway present in some bacterial and apicomplexans but distinct from that used by mammals. Our analysis reveals a homotrimer, built around a ␤ prism, carrying three active sites, each of which is formed in a cleft between pairs of subunits. Residues from two subunits recognize and bind the nucleotide in an active site that contains a Zn 2؉ with tetrahedral coordination. A Mn 2؉ , with octahedral geometry, is positioned between the ␣ and ␤ phosphates acting in concert with the Zn 2؉ to align and polarize the substrate for catalysis. A high degree of sequence conservation for the enzymes from E. coli, Plasmodium falciparum, and Mycobacterium tuberculosis suggests similarities in secondary structure, subunit fold, quaternary structure, and active sites. Our model will therefore serve as a template to facilitate the structurebased design of potential antimicrobial agents targeting two of the most serious human diseases, tuberculosis and malaria.zinc enzyme ͉ Escherichia coli ͉ Plasmodium falciparum ͉ Mycobacterium tuberculosis T he enzyme 2C-methyl-D-erythritol 2,4-cyclodiphosphate (MECP) synthase participates in the biosynthesis of the isomers isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate. These compounds are the universal five-carbon precursors of isoprenoids, a diverse and large family of natural products including sterols, dolichols, triterpenes, ubiquinones, and plastoquinone, and also components of macromolecules such as the prenyl groups of prenylated proteins and isopentenylated tRNAs (1-3). Isoprenoids contribute to many functions, including electron transport in respiration and photosynthesis, hormone-based signaling, the regulation of transcription, and posttranslational processes that control lipid biosynthesis, meiosis, apoptosis, protein cleavage, and degradation. In addition, certain isoprenoids constitute an important structural component of cell membranes.Isoprenoid biosynthesis depends on the production of IPP, which occurs in mammals, higher plants, fungi, and certain bacteria through the mevalonate (MVA) pathway (4-7). This pathway begins with the conversion of acetyl-CoA to 3-hydroxy-3-methylglutaryl-CoA, followed by reduction, phosphorylation, and decarboxylation to generate IPP, some of which is then isomerized to dimethylallyl pyrophosphate. The MVA pathway was considered ubiquitous until recently, when a nonmevalonate-dependent route, the 1-deoxy-D-xylulose 5-phosphate (DOXP) or 2C-methyl-D-erythritol 4-phosphate (MEP) pathway, was discovered in chloroplasts, algae, cyanobacteria, eubacteria, and apicomplexa (2, 6, 7).Five distinct steps of the DOXP͞MEP pathway have been elucidated (6-10). The pathway starts with the condensation of pyruvate and glyceralde...

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“…13 C NMR spectra were recorded at intervals. Residues involved in substrate binding [31][32][33] are labeled by triangles; conserved residues are shown in grey, identical residues in black. Kinetic studies on recombinant IspDF protein by NMR spectroscopy 13 C NMR signal intensities were used to perform numerical simulations using the program DYNAFIT [30].…”

Section: Nmr Assay For Ispf Activitymentioning

confidence: 99%

Biosynthesis of isoprenoids

Gabrielsen

Rohdich

Eisenreich

et al. 2004

European Journal of Biochemistry

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In the nonmevalonate pathway of isoprenoid biosynthesis, the conversion of 2C-methyl-D-erythritol 4-phosphate into its cyclic diphosphate proceeds via nucleotidyl intermediates and is catalyzed by the products of the ispD, ispE and ispF genes. An open reading frame of Campylobacter jejuni with similarity to the ispD and ispF genes of Escherichia coli was cloned into an expression vector directing the formation of a 42 kDa protein in a recombinant E. coli strain. The purified protein was shown to catalyze the transformation of 2C-methyl-D-erythritol 4-phosphate into 4-diphosphocytidyl-2C-methyl-D-erythritol and the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate into 2C-methyl-D-erythritol 2,4-cyclodiphosphate at catalytic rates of 19 lmolAEmg )1 AEmin )1 and 7 lmolAEmg )1 AEmin )1 , respectively. Both enzyme-catalyzed reactions require divalent metal ions. The C. jejuni enzyme does not catalyze the formation of 2C-methyl-D-erythritol 3,4-cyclophosphate from 4-diphosphocytidyl-2C-methyl-D-erythritol, a side reaction catalyzed in vitro by the IspF proteins of E. coli and Plasmodium falciparum. Comparative genomic analysis show that all sequenced a-and e-proteobacteria have fused ispDF genes. These bifunctional proteins are potential drug targets in several human pathogens (e.g. Helicobacter pylori, C. jejuni and Treponema pallidum).

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Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids

Cited by 76 publications

References 34 publications

Biosynthesis of isoprenoids: Crystal structure of 4-diphosphocytidyl-2C-methyl- d -erythritol kinase

Biosynthesis of isoprenoids: Crystal structure of 4-diphosphocytidyl-2C-methyl- d -erythritol kinase

Structure of 2C-methyl- d -erythritol 2,4- cyclodiphosphate synthase: An essential enzyme for isoprenoid biosynthesis and target for antimicrobial drug development

Biosynthesis of isoprenoids

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