(2R)-CDP-glycerol(2-)

• 分子结构分类: 有机化合物 - 脂质和类脂质分子 - 甘油磷脂
• 英文名称: (2R)-CDP-glycerol(2-)
• 英文别名: [[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-oxidophosphoryl] [(2R)-2,3-dihydroxypropyl] phosphate
• 化学式: C12H19N3O13P2-2
• 分子量: 475.24
• InChiKey: HHPOUCCVONEPRK-JBSYKWBFSA-L

计算性质

• 辛醇/水分配系数(LogP)：
  -5.4
• 重原子数：
  30
• 可旋转键数：
  10
• 环数：
  2.0
• sp3杂化的碳原子比例：
  0.67
• 拓扑面积：
  257
• 氢给体数：
  5
• 氢受体数：
  13

反应信息

• 作为反应物：
  描述：

  (2R)-CDP-glycerol(2-) 、 水 生成 cytidine 5'-monophosphate 、 氢(+1)阳离子 、 L-Glycerin-3-phosphat
  参考文献：
  名称：

  Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase: a novel metallophosphoesterase family preferentially expressed in rodent immune cells

  摘要：

  ADPRibase-Mn （Mn2+ 依赖性 ADP-ribose/CDP-alcohol 焦磷酸酶）是早些时候从大鼠肝脏上清液中分离出来的，分离后的 ADPRibase-I 和 ADPRibase-II（Mg2+ 激活的 ADP-ribose 焦磷酸酶，无 CDP-alcohol 焦磷酸酶活性）。最后提到的是推定的 Nudix 水解酶，而 ADPRibase-Mn 的分子特征尚不清楚。大鼠 ADPRibase-Mn 的 MALDI（基质辅助激光解吸电离）质谱数据表明，它是一种克隆和表达的假定蛋白，并显示出预期的特异性。它由 RGD1309906 大鼠基因编码，迄今为止该基因仅被注释为 "水解酶"。ADPRibase-Mn 不是一种 Nudix 水解酶，但它显示出金属磷酸酯酶超家族的典型序列和结构特征。它可能自成一个蛋白家族，其成员似乎是脊椎动物、植物和藻类特有的。ADP-ribose 与大鼠 ADPRibase-Mn 的模型对接成功，揭示了其推定的活性中心。来自 GEO（基因表达总库）数据库的微阵列数据表明，RGD1309906 的同源基因小鼠基因 2310004I24Rik 优先在免疫细胞中表达。大鼠组织中的 Northern-blot 和 ADPRibase-Mn 活性测定证实了这一点。ADP-ribose 可激活 TRPM2（瞬时受体电位美司他丁通道-2）离子通道，成为氧化/亚硝基应激的介质，而 2310004I24Rik 的许多微阵列图谱邻域都具有信号功能，这表明 ADPRibase-Mn 可能在免疫细胞信号中发挥作用。此外，还不能排除 ADPRibase-Mn 对磷脂生物合成的 CDP-choline 或 CDP-ethanolamine 途径的影响。

  DOI：

  10.1042/bj20071471
• 作为产物：
  描述：

  cytidine 5'-triphosphate 、 氢(+1)阳离子 、 L-Glycerin-3-phosphat 生成 (2R)-CDP-glycerol(2-) 、 pyrophosphoric acid
  参考文献：
  名称：

  Negative Cooperativity of Substrate Binding but Not Enzyme Activity in Wild-type and Mutant Forms of CTP:Glycerol-3-Phosphate Cytidylyltransferase

  摘要：

  CTP:glycerol-3-phosphate cytidylyltransferase (GCT) catalyzes the synthesis of CDP-glycerol for teichoic acid biosynthesis in certain Gram-positive bacteria. This enzyme is a model for a cytidylyltransferase family that includes the enzymes that synthesize CDP-choline and CDP-ethanolamine for phosphatidylcholine and phosphatidylethanolamine biosynthesis. We have used quenching of intrinsic tryptophan fluorescence to measure binding affinities of substrates to the GCT from Bacillus subtilis. Binding of either CTP or glycerol-3-phosphate to GCT was biphasic, with two binding constants of about 0.1-0.3 and 20-40 microm for each substrate. The stoichiometry of binding was 2 molecules of substrate/enzyme dimer, so the two binding constants represented distinctly different affinities of the enzyme for the first and second molecule of each substrate. The biphasic nature of binding was observed with the wild-type GCT as well as with several mutants with altered Km or kcat values. This negative cooperativity of binding was also seen when a catalytically defective mutant was saturated with two molecules of CTP and then titrated with glycerol-3-phosphate. Despite the pronounced negative cooperativity of substrate binding, negative cooperativity of enzyme activity was not observed. These data support a mechanism in which catalysis occurs only when the enzyme is fully loaded with 2 molecules of each substrate/enzyme dimer.

  DOI：

  10.1074/jbc.m107198200

文献信息

• A Revised Pathway Proposed for Staphylococcus aureus Wall Teichoic Acid Biosynthesis Based on In Vitro Reconstitution of the Intracellular Steps
  作者：Stephanie Brown、Yu-Hui Zhang、Suzanne Walker

  DOI：10.1016/j.chembiol.2007.11.011

  日期：2008.1

  clinically used antibiotics has emerged, and there is a pressing need to explore unique antibacterial targets. Wall teichoic acids (WTAs) are anionic polymers that coat the cell walls of many Gram-positive bacteria. Because WTAs play an essential role inStaphylococcus aureuscolonization and infection, the enzymes involved in WTA biosynthesis are proposed to be targets for antibiotic development. To

  对临床使用的每一个抗生素家族都出现了耐药性，迫切需要探索独特的抗菌靶点。壁磷壁酸 (WTA) 是阴离子聚合物，可覆盖许多革兰氏阳性细菌的细胞壁。由于 WTA 在金黄色葡萄球菌的定植和感染中起重要作用，因此建议将参与 WTA 生物合成的酶作为抗生素开发的目标。为了促进 WTA 抑制剂的发现，我们重构了金黄色葡萄球菌 WTA 生物合成的细胞内步骤。我们表明生物合成途径中的两个细胞内步骤与所提出的不同。此处报告的工作为发现和表征 WTA 生物合成酶抑制剂以评估其治疗细菌感染的潜力奠定了基础。
• CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase, which is involved in the synthesis of the major wall teichoic acid in Bacillus subtilis 168, is encoded by tagF (rodC)
  作者：H M Pooley、F X Abellan、D Karamata

  DOI：10.1128/jb.174.2.646-649.1992

  日期：1992.1

  Assays of CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase (CGPTase) (EC 2.7.8.12) in membranes isolated from Bacillus subtilis 168 wild type and 11 strains bearing conditional lethal thermosensitive mutations in tagB, tagD, or tagF revealed that CGPTase deficiency was associated only with mutant tagF alleles. In vitro, thermosensitivity of CGPTase strongly suggests that the structural gene for this enzyme is tagF. We discuss apparent discrepancies between biochemical evidence favoring a membrane location for TagF and a previous report that suggested a cytoplasmic location based on sequence analysis.

  从Bacillus subtilis 168野生型和11株携带tagB、tagD或tagF条件致死温敏突变的菌株分离的膜中检测CDP-甘油：聚（甘油磷酸）甘油磷酸转移酶（CGPTase）（EC 2.7.8.12）的测定结果表明，CGPTase缺陷仅与突变的tagF等位基因相关。体外实验表明，CGPTase的温敏性强烈暗示了这种酶的结构基因是tagF。我们讨论了表观上有关TagF有利于膜位置的生化证据和先前报告基于序列分析表明它位于细胞质位置之间的明显差异。
• Structure of the bacterial teichoic acid polymerase TagF provides insights into membrane association and catalysis
  作者：Andrew L Lovering、Leo Y-C Lin、Edward W Sewell、Thomas Spreter、Eric D Brown、Natalie C J Strynadka

  DOI：10.1038/nsmb.1819

  日期：2010.5

  Gram-positive bacteria have a thick cell wall composed of peptidoglycan and teichoic acid, a complex anionic polymer that is important for cellular integrity and virulence. The crystal structures of TagF polymerase from Staphylococcus epidermidis in its apo form and in complex with a model susbtrate are now presented, providing insight into teichoic acid biosynthesis. Teichoic acid polymers are composed of polyol-phosphate units and form a major component of Gram-positive bacterial cell walls. These anionic compounds perform a multitude of important roles in bacteria and are synthesized by monotopic membrane proteins of the TagF polymerase family. We have determined the structure of Staphylococcus epidermidis TagF to 2.7-Å resolution from a construct that includes both the membrane-targeting region and the glycerol-phosphate polymerase domains. TagF possesses a helical region for interaction with the lipid bilayer, placing the active site at a suitable distance for access to the membrane-bound substrate. Characterization of active-site residue variants and analysis of a CDP-glycerol substrate complex suggest a mechanism for polymer synthesis. With the importance of teichoic acid in Gram-positive physiology, this elucidation of the molecular details of TagF function provides a critical new target in the development of novel anti-infectives.

  革兰氏阳性细菌具有由肽聚糖和粘多糖酸组成的厚细胞壁，粘多糖酸是一种复杂的阴离子聚合物，对细胞完整性和致病性至关重要。现已呈现表皮葡萄球菌TagF聚合酶的晶状结构，包括其游离形式和与模型底物的复合物，为了解粘多糖酸的生物合成提供了线索。粘多糖酸聚合物由多元醇磷酸单元组成，是革兰氏阳性细菌细胞壁的主要成分。这些阴离子化合物在细菌中发挥着多种重要作用，由TagF聚合酶家族的单一膜蛋白合成。我们已确定表皮葡萄球菌TagF的结构，其分辨率达到2.7Å，构建体包括膜靶向区域和甘油磷酸聚合酶结构域。TagF具有与脂质双层相互作用的螺旋区域，将活性位点置于合适的距离，以便接触膜结合底物。活性位点残基变体的表征和CDP-甘油底物复合物的分析为聚合物的合成提供了机制。鉴于粘多糖酸在革兰氏阳性生理学中的重要性，TagF功能的分子细节阐明为新型抗感染药物的开发提供了关键的新靶点。
• Purified, Recombinant TagF Protein from Bacillus subtilis 168 Catalyzes the Polymerization of Glycerol Phosphate onto a Membrane Acceptor in Vitro
  作者：Jeffrey W. Schertzer、Eric D. Brown

  DOI：10.1074/jbc.m300706200

  日期：2003.5

  characterization of a recombinant protein involved in the polymerization of wall teichoic acid. Previously, a study of the teichoic acid polymerase activity associated with membranes from Bacillus subtilis 168 strains bearing thermosensitive mutations in tagB, tagD, and tagF implicated TagF as the poly(glycerol phosphate) polymerase (Pooley, H. M., Abellan, F. X., and Karamata, D. (1992) J. Bacteriol. 174

  我们报告了参与墙壁chochochoic酸的聚合反应的重组蛋白的首次表征。以前，一项针对与枯草芽孢杆菌168菌株膜相关的海胆酸聚合酶活性的研究，该菌株在tagB，tagD和tagF中带有热敏突变，将TagF关联为聚磷酸甘油酯聚合酶（Pooley，HM，Abellan，FX和Karamata， D.（1992）J. Bacteriol。174，646-649）。在本文报道的工作中，我们已经证明了tagF在一个突变体（tagF1）的热敏性中具有明确的作用，该突变体是在木糖启动子的控制下，在amyE基因座的控制下，在限制性温度下与tagF有条件地互补的。我们已经过表达和纯化了重组枯草芽孢杆菌TagF蛋白，并且我们提供了直接的生化证据，表明该酶负责枯草芽孢杆菌168中聚磷酸甘油酸的聚合。重组六组氨酸标签的TagF蛋白是从大肠杆菌中纯化的，并用于开发新型膜沉淀法来监测聚磷酸甘油酯聚合酶活性。纯化的T
• Two Conserved Histidine Residues Are Critical to the Function of the TagF-like Family of Enzymes
  作者：Jeffrey W. Schertzer、Amit P. Bhavsar、Eric D. Brown

  DOI：10.1074/jbc.m507153200

  日期：2005.11

  The TagF protein from Bacillus subtilis 168 is the poly(glycerol phosphate) polymerase responsible for the synthesis of wall teichoic acid and is the prototype member of a poorly understood family of similar teichoic acid synthetic enzymes. Here we describe in vitro and in vivo characterization of TagF, which localizes the active site to the carboxyl terminus of the protein and identifies residues

  枯草芽孢杆菌168的TagF蛋白是负责壁壁壁壁酸的合成的聚（磷酸甘油）聚合酶，并且是人们所知甚少的相似壁壁酸合成酶家族的原型成员。在这里，我们描述了TagF的体外和体内表征，该特征将活性位点定位在蛋白质的羧基末端，并鉴定对于催化至关重要的残基。我们还通过证明已鉴定的残基在TagB的功能中也很关键来建立TagF和类似蛋白质之间的第一个机械联系，TagB是一种牵涉引发甘油磷酸磷酸酯的甘油磷酸转移酶的同源酶。我们调查了TagF活性对pH的依赖性，并表明带有pK（a）的残基的去质子接近中性对于适当的功能至关重要。通过定点诱变改变组氨酸残基474和612消除了TagF的体外活性（k（cat）/ K（m）降低了5000倍），而其他四个保守的酸性残基的变体显示出最小的活性损失。使用H474A和H612A突变等位基因的互补不能抑制致命的温度敏感tagF缺陷体内，尽管已通过Western blot证实了其强