CDP-ME2P

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘧啶核苷酸
• 英文名称: CDP-ME2P
• 英文别名: 4-CDP-2-C-methyl-D-erythritol 2-phosphate(4-)；[(2S,3R)-4-[[[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-oxidophosphoryl]oxy-oxidophosphoryl]oxy-1,3-dihydroxy-2-methylbutan-2-yl] phosphate
• 化学式: C₁₄H₂₂N₃O₁₇P₃
• 分子量: 597.26
• InChiKey: HTJXTKBIUVFUAR-XHIBXCGHSA-J

计算性质

• 辛醇/水分配系数(LogP)：
  -7.1
• 重原子数：
  37
• 可旋转键数：
  12
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.71
• 拓扑面积：
  329
• 氢给体数：
  5
• 氢受体数：
  17

反应信息

• 作为反应物：
  描述：

  CDP-ME2P 在 pyruvate kinase 、 2-methylerythritol 2,4-cyclodiphosphate synthase from Mycobacterium tuberculosis 、 cytidine 5'-monophosphate kinase 、 (+/-)-ethyl (2Z)-5-(1-benzofuran-2-yl)-2-(3,5-dibromo-4-hydroxybenzylidene)-7-methyl-3-oxo-2,3-dihydro-5H-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxylate 、 NADH 、 phosphoenol pyruvate 、 adenosine 5'-triphosphate disodium salt 、 magnesium chloride 、 L-lactate dehydrogenase 作用下， 生成 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
  参考文献：
  名称：

  结核分枝杆菌和恶性疟原虫的2-甲基赤藓糖醇2,4-环二磷酸合酶（IspF）的噻唑并嘧啶抑制剂

  摘要：

  使用光度测定法筛选了一个来自40 000个化合物的文库，以筛选拟南芥中的2-甲基赤藓糖醇2,4-环二磷酸合酶（IspF）蛋白的抑制剂。高通量筛选产生的噻唑并嘧啶衍生物可抑制结核分枝杆菌，恶性疟原虫和拟南芥的IspF蛋白，其IC 50值在微摩尔范围内。合成努力提供了抑制结核分枝杆菌和恶性疟原虫IspF蛋白的衍生物，其IC 50值在低微摩尔范围内。几种化合物在恶性疟原虫中充当弱抑制剂红细胞分析。

  DOI：

  10.1002/cmdc.201000083
• 作为产物：
  描述：

  5’-三磷酸腺苷 、 4-diphosphocytidyl-2-C-methyl-D-erythritol 在 magnesium chloride 作用下， 生成 CDP-ME2P
  参考文献：
  名称：

  Expression and Characterization of Soluble 4-Diphosphocytidyl-2-C-methyl-D-erythritol Kinase from Bacterial Pathogens

  摘要：

  Many bacterial pathogens utilize the 2-C-methyl-D-erythritol 4-phosphate pathway for biosynthesizing isoprenoid precursors, a pathway that is vital for bacterial survival and absent from human cells, providing a potential source of drug targets. However, the characterization of 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDP-ME) kinase (IspE) has been hindered due to a lack of enantiopure CDP-ME and difficulty in obtaining pure IspE. Here, enantiopure CDP-ME was chemically synthesized and recombinant IspE from bacterial pathogens were purified and characterized. Although gene disruption was not possible in Mycobacterium tuberculosis, IspE is essential in Mycobacterium smegmatis. The biochemical and kinetic characteristics of IspE provide the basis for development of a high throughput screen and structural characterization.

  DOI：

  10.1016/j.chembiol.2009.10.014

文献信息

• Synthesis of 4-Diphosphocytidyl-2-C-Methyl-D-Erythritol 2-Phosphate and Kinetic Studies of Mycobacterium tuberculosis IspF
  作者：Prabagaran Narayanasamy、Hyungjin Eoh、Patrick J. Brennan、Dean C. Crick

  DOI：10.1016/j.chembiol.2010.01.013

  日期：2010.2

  Many pathogenic bacteria utilize the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for the biosynthesis of isopentenyl diphosphate and dimethylallyl diphosphate, two major building blocks of isoprenoid compounds. The fifth enzyme in the MEP pathway, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) synthase (IspF), catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate

  许多病原菌利用 2-C-甲基-D-赤藓糖醇 4-磷酸 (MEP) 途径生物合成异戊二烯基二磷酸和二甲基烯丙基二磷酸，这是类异戊二烯化合物的两个主要组成部分。MEP 途径中的第五种酶，2-C-甲基-D-赤藓糖醇 2,4-环二磷酸 (ME-CPP) 合酶 (IspF)，催化 4-二磷酸胞苷-2-C-甲基-D-赤藓糖醇 2 的转化-磷酸盐 (CDP-ME2P) 转化为 ME-CPP，相应地释放胞苷 5-单磷酸盐 (CMP)。由于人类细胞中没有 IspF 的直系同源物，因此 IspF 作为潜在的药物靶点很受关注。然而，由于缺乏对映体纯 CDP-ME2P，IspF 的研究受到阻碍。在此，我们首次报道了从市售 D-阿拉伯糖合成对映异构纯 CDP-ME2P。克隆、表达和纯化 M. 结核分枝杆菌能够利用合成的 CDP-ME2P 作为底物，这一结果由质谱法证实。通过将 ME-CPP 生产过程中释放的 CMP
• Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl- <scp>d</scp> -erythritol 2-phosphate to 2C-methyl- <scp>d</scp> -erythritol 2,4-cyclodiphosphate
  作者：Stefan Herz、Juraithip Wungsintaweekul、Christoph A. Schuhr、Stefan Hecht、Holger Lüttgen、Sylvia Sagner、Monika Fellermeier、Wolfgang Eisenreich、Meinhart H. Zenk、Adelbert Bacher、Felix Rohdich

  DOI：10.1073/pnas.040554697

  日期：2000.3.14

  In many microorganisms, the putative orthologs of the Escherichia coli ygbB gene are tightly linked or fused to putative orthologs of ygbP , which has been shown earlier to be involved in terpenoid biosynthesis. The ygbB gene of E. coli was expressed in a recombinant E. coli strain and was shown to direct the synthesis of a soluble, 17-kDa polypeptide. The recombinant protein was found to convert 4-diphosphocytidyl-2C-methyl- d -erythritol 2-phosphate into 2C-methyl- d -erythritol 2,4-cyclodiphosphate and CMP. The structure of the reaction product was established by NMR spectroscopy using ¹³ C-labeled substrate samples. The enzyme-catalyzed reaction requires Mn ²⁺ or Mg ²⁺ but no other cofactors. Radioactivity from [2- ¹⁴ C]2C-methyl- d -erythritol 2,4-cyclodiphosphate was diverted efficiently to carotenoids by isolated chromoplasts from Capsicum annuum and, thus, was established as an intermediate in the deoxyxylulose phosphate pathway of isoprenoid biosynthesis. YgbB protein also was found to convert 4-diphosphocytidyl-2C-methyl- d -erythritol into 2C-methyl- d -erythritol 3,4-cyclophosphate. This compound does not serve as substrate for the formation of carotenoids by isolated chromoplasts and is assumed to be an in vitro product without metabolic relevance.

  在许多微生物中，Escherichia coli的ygbB基因的推定同源物通常与ygbP的推定同源物紧密链接或融合在一起，而ygbP早已被证明参与萜类化合物的生物合成。大肠杆菌的ygbB基因在重组的大肠杆菌菌株中表达，并被证明可以指导合成一种可溶性的17 kDa多肽。发现重组蛋白质可以将4-二磷酸胞苷基-2C-甲基-d-赤藓糖醇2-磷酸转化为2C-甲基-d-赤藓糖醇2,4-环二磷酸和CMP。使用13C标记的底物样品，通过NMR光谱法确定了反应产物的结构。酶催化的反应需要Mn2+或Mg2+，但不需要其他辅因子。[2-14C]2C-甲基-d-赤藓糖醇2,4-环二磷酸的放射性能有效地被辣椒素细胞色素体转化为类胡萝卜素，并因此被确定为异戊烯类化合物生物合成的去氧木糖磷酸途径的中间体。发现YgbB蛋白还可以将4-二磷酸胞苷基-2C-甲基-d-赤藓糖醇转化为2C-甲基-d-赤藓糖醇3,4-环磷酸。这种化合物不能作为细胞色素体形成类胡萝卜素的底物，被认为是一种无代谢相关的体外产物。
• 2<i>C</i>-Methyl-<scp>d</scp>-erythritol 4-Phosphate Enhances and Sustains Cyclodiphosphate Synthase IspF Activity
  作者：J. Kipchirchir Bitok、Caren Freel Meyers

  DOI：10.1021/cb300243w

  日期：2012.10.19

  significant progress toward understanding catalysis throughout the essential MEP pathway to isoprenoids in human pathogens; however, little is known about pathway regulation. The present study begins by testing the hypothesis that isoprenoid biosynthesis is regulated via feedback inhibition of the fifth enzyme cyclodiphosphate synthase IspF by downstream isoprenoid diphosphates. Here, we demonstrate recombinant

  在理解人类病原体中类异戊二烯的基本 MEP 途径中的催化作用方面取得了重大进展；然而，对通路调节知之甚少。本研究开始通过测试该异戊二烯生物合成调节的假设经由第五酶环二合酶ISPF的反馈抑制由下游类异戊二烯基二磷酸。在这里，我们证明了重组大肠杆菌IspF 在标准测定条件下不受下游代谢物异戊烯基二磷酸 (IDP)、二甲基烯丙基二磷酸 (DMADP)、香叶基二磷酸 (GDP) 和法呢基二磷酸 (FDP) 的抑制。然而，2 Ç甲基d-赤藓糖醇 4-磷酸 (MEP)，还原异构酶 IspC 的产物和第一个定型 MEP 途径中间体，激活并维持这种增强的 IspF 活性，并且 IspF-MEP 复合物被 FDP 抑制。我们进一步表明，该途径独有的甲基赤藓糖醇支架本身驱动活性 IspF 的激活和稳定。我们的结果显示为2的新的前馈调节机制Ç甲基d -赤2,4-环（MECDP）的生产和支持异戊二烯生物合成的调节
• Biosynthesis of terpenoids: YchB protein of <i>Escherichia coli</i> phosphorylates the 2-hydroxy group of 4-diphosphocytidyl-2C-methyl- <scp>d</scp> -erythritol
  作者：Holger Lüttgen、Felix Rohdich、Stefan Herz、Juraithip Wungsintaweekul、Stefan Hecht、Christoph A. Schuhr、Monika Fellermeier、Sylvia Sagner、Meinhart H. Zenk、Adelbert Bacher、Wolfgang Eisenreich

  DOI：10.1073/pnas.97.3.1062

  日期：2000.2

  A comparative analysis of all published complete genomes indicated that the putative orthologs of the unannotated ychB gene of Escherichia coli follow the distribution of the dxs , dxr , and ygbP genes, which have been shown to specify enzymes of the deoxyxylulose phosphate pathway of terpenoid biosynthesis, thus suggesting that the hypothetical YchB protein also is involved in that pathway. To test this hypothesis, the E. coli ychB gene was expressed in a homologous host. The recombinant protein was purified to homogeneity and was shown to phosphorylate 4-diphosphocytidyl-2C-methyl- d -erythritol in an ATP-dependent reaction. The reaction product was identified as 4-diphosphocytidyl-2C-methyl- d -erythritol 2-phosphate by NMR experiments with various ¹³ C-labeled substrate samples. A ¹⁴ C-labeled specimen of this compound was converted efficiently into carotenoids by isolated chromoplasts of Capsicum annuum . The sequence of E. coli YchB protein is similar to that of the protein predicted by the tomato cDNA pTOM41 (30% identity), which had been implicated in the conversion of chloroplasts to chromoplasts.

  对所有已发表的完整基因组进行比较分析表明，大肠杆菌未注释的ychB基因的推测同源基因遵循了dxs、dxr和ygbP基因的分布，这些基因已被证明是萜类生物合成中脱氧木糖磷酸途径酶的指定基因，因此暗示假设的YchB蛋白也参与了该途径。为了验证这一假设，将大肠杆菌ychB基因在同源宿主中表达。重组蛋白被纯化至同质性，并显示出在ATP依赖性反应中磷酸化4-二磷酸胞苷-2C-甲基-d-赤藓糖。通过使用各种13C标记底物样品的NMR实验，将反应产物鉴定为4-二磷酸胞苷-2C-甲基-d-赤藓糖2-磷酸酯。这种化合物的14C标记标本被分离的辣椒色素体高效地转化为类胡萝卜素。大肠杆菌YchB蛋白的序列与番茄cDNA pTOM41预测的蛋白的序列相似（30%的同源性），后者已被认为参与了叶绿体向色素体的转化。
• Biosynthesis of isoprenoids
  作者：Mads Gabrielsen、Felix Rohdich、Wolfgang Eisenreich、Tobias Gräwert、Stefan Hecht、Adelbert Bacher、William N. Hunter

  DOI：10.1111/j.1432-1033.2004.04234.x

  日期：——

  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 µmol·mg−1·min−1 and 7 µmol·mg−1·min−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 α‐ and ε‐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).