dTDP-α-Glc

• 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: dTDP-α-Glc
• 英文别名: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-4-oxido-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [hydroxy-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphosphoryl] phosphate
• 化学式: C₁₆H₂₄N₂O₁₆P₂
• 分子量: 562.318
• InChiKey: YSYKRGRSMLTJNL-URARBOGNSA-L

计算性质

• 辛醇/水分配系数(LogP)：
  -5.7
• 重原子数：
  36
• 可旋转键数：
  9
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.75
• 拓扑面积：
  277
• 氢给体数：
  6
• 氢受体数：
  16

反应信息

• 作为反应物：
  描述：

  dTDP-α-Glc 在 RfbB enzyme 作用下， 反应 1.0h， 生成 TDP-4-keto-6-deoxy-D-glucose
  参考文献：
  名称：

  DesII 的表征和机理研究：一种参与 TDP-d-Desosamine 生物合成的自由基 S-腺苷-l-甲硫氨酸酶

  摘要：

  D-脱糖胺 (1) 是一种 3-(N,N-二甲氨基)-3,4,6-三脱氧己糖，存在于多种大环内酯类抗生素中，包括甲霉素 (2)、新甲霉素 (3)、匹克霉素 (4) 和纳博霉素(5)由委内瑞拉链霉菌产生。它在赋予其亲本苷元生物活性方面发挥着重要作用。以前对委内瑞拉沙门氏菌中去糖胺生物合成的遗传和生化研究表明，TDP-4-amino-4,6-dideoxy-D-glucose (8) 转化为 TDP-3-keto-4,6-dideoxy- D-葡萄糖 (9) 由 DesII 催化，DesII 是自由基 S-腺苷-L-甲硫氨酸 (SAM) 酶超家族的成员。在这里，我们报告了 His(6) 标记的 DesII 的纯化和重建，使用 UV-vis 和 EPR 光谱对其 [4Fe-4S] 簇的表征，以及黄素氧还蛋白、黄素氧还蛋白还原酶、和 NADPH 以减少 [4Fe-4S](2+) 簇。还包括 DesII

  DOI：

  10.1021/ja903354k
• 作为产物：
  描述：

  5-nitro-cyclosaligenyl-3'-O-acetylthymidine monophosphate 、 2,3,4,6-tetra-O-acetyl-α-D-glucopyranosyl-1-phosphate triethylammonium salt 在 三乙胺 作用下， 以 N,N-二甲基甲酰胺 、 甲醇 、 水 为溶剂， 反应 12.0h， 以60%的产率得到dTDP-α-Glc
  参考文献：
  名称：

  有效合成核苷二磷酸吡喃葡萄糖。

  摘要：

  DOI：

  10.1002/anie.200703237

文献信息

• Purification and Characterization of UDP-glucose:Ceramide Glucosyltransferase from Rat Liver Golgi Membranes
  作者：Pascal Paul、Yasushi Kamisaka、David L. Marks、Richard E. Pagano

  DOI：10.1074/jbc.271.4.2287

  日期：1996.1

  (GCS) from a rat liver and present data on its substrate specificity. A Golgi membrane fraction was isolated, washed with N-lauroylsarcosine, and subsequently treated with 3[3-cholamidopropyl)-dimethylammonio]-2-hydroxy-1-propanesulfonate to solubilize the enzyme. GCS activity was monitored throughout purification using UDP-Glc and a fluorescent ceramide analog as substrates. Purification of GCS was

  我们提出了一种从大鼠肝脏中溶解和纯化UDP-Glc：神经酰胺葡糖基转移酶（EC 2.4.1.80;葡糖神经酰胺合酶（GCS））的方法，并提供了其底物特异性的数据。分离了高尔基体膜部分，用N-月桂酰肌氨酸洗涤，然后用3 [3-胆酰胺丙基）-二甲基铵-2-羟基-1-丙烷磺酸盐处理以溶解该酶。在整个纯化过程中，使用UDP-Glc和荧光神经酰胺类似物作为底物，监控GCS活性。GCS的纯化是通过使用UDP-Glc洗脱酶的两步染料-琼脂糖色谱法完成的。相对于起始匀浆，这导致富集> 10,000倍。通过在甘油梯度上沉淀，I标记和SDS-聚丙烯酰胺凝胶电泳进一步表征该酶。表明两个多肽（60-70 kDa）与GCS活性密切相关。发现纯化的GCS需要外源的磷脂才能发挥活性，使用二油酰基磷脂酰胆碱可获得最佳结果。对纯化的酶的底物特异性的研究表明，它是立体特异性的，并且取决于N-酰基-亚鞘氨醇或-鞘氨醇底物的性质
• Genetic analysis of the dTDP-rhamnose biosynthesis region of the Escherichia coli VW187 (O7:K1) rfb gene cluster: identification of functional homologs of rfbB and rfbA in the rff cluster and correct location of the rffE gene
  作者：C L Marolda、M A Valvano

  DOI：10.1128/jb.177.19.5539-5546.1995

  日期：1995.10

  The O-repeating unit of the Escherichia coli O7-specific lipopolysaccharide is made of galactose, mannose, rhamnose, 4-acetamido-4,6-dideoxyglucose, and N-acetyglucosamine. We have recently characterized the genes involved in the biosynthesis of the sugar precursor GDP-mannose occurring in the E. coli O7:K1 strain VW187 (C. L. Marolda and M. A. Valvano, J. Bacteriol. 175:148-158, 1993). In the present study, we identified and sequenced the rfbBDAC genes encoding the enzymes for the biosynthesis of another precursor, dTDP-rhamnose. These genes are localized on the upstream end of the rfbEcO7 region, and they are strongly conserved compared with similar genes found in various enteric and nonenteric bacteria. Upstream of rfbB we identified a DNA segment containing the rfb promoter and a highly conserved untranslated leader sequence also present in the promoter regions of other surface polysaccharide gene clusters. Also, we have determined that rfbB and rfbA have homologs, rffG (o355) and rffH (o292), respectively, located on the rff cluster, which is involved in the synthesis of enterobacterial common antigen. We provide biochemical evidence that rffG and rffH encode dTDP-glucose dehydratase and glucose-1-phosphate thymidylyltransferase activities, respectively, and we also show that rffG complemented the rfbB defect in the O7+ cosmid pJHCV32. We also demonstrate that rffG is distinct from rffE and map the rffE gene to the second gene of the rff cluster.

  大肠杆菌O7专属脂多糖的O-重复单元由半乳糖、甘露糖、鼠李糖、4-乙酰胺基-4,6-二脱氧葡萄糖和N-乙酰葡萄糖胺组成。我们最近鉴定了参与E. coli O7:K1菌株VW187中GDP-甘露糖前体生物合成的基因（C.L. Marolda和M.A. Valvano，J. Bacteriol. 175:148-158，1993）。在本研究中，我们确定并测序了rfbBDAC基因，这些基因编码另一种前体dTDP-鼠李糖的生物合成酶。这些基因位于rfbEcO7区域的上游端，与在各种肠道和非肠道细菌中发现的类似基因相比，它们具有很强的保守性。在rfbB的上游，我们确定了一个DNA片段，其中包含rfb启动子和高度保守的未翻译的领导序列，这些序列也存在于其他表面多糖基因簇的启动子区域中。此外，我们确定了rfbB和rfbA的同源基因rfFG（o355）和rfFH（o292），它们分别位于rfF群集中，参与肠道细菌共同抗原的合成。我们提供了生化证据表明rfFG和rfFH分别编码dTDP-葡萄糖脱水酶和葡萄糖-1-磷酸己糖基转移酶活性，并且我们还展示了rfFG在O7 + cosmid pJHCV32中补充了rfbB缺陷。我们还证明了rfFG与rfFE不同，并将rfFE基因定位于rfF群集的第二个基因。
• Kinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase
  作者：Simone Zuccotti、Davide Zanardi、Camillo Rosano、Laura Sturla、Michela Tonetti、Martino Bolognesi

  DOI：10.1006/jmbi.2001.5073

  日期：2001.11

  more light on the catalytic properties of glucose-1-phosphate thymidylyltransferase from Escherichia coli, specifically distinguishing between ping pong and sequential ordered bi bi reaction mechanisms, the enzyme kinetic properties have been analysed in the presence of different substrates and inhibitors. Moreover, three different complexes of glucose-1-phosphate thymidylyltransferase (co-crystallized

  1-磷酸葡萄糖胸苷基转移酶是dTDP-1-鼠李糖（l-鼠李糖的前体）的生物合成中的第一种酶，它是表面抗原（例如O-脂多糖）的重要成分，在许多组织中介导毒力和对宿主组织的粘附。微生物。该酶催化dTTP和1-磷酸葡萄糖形成dTDP-葡萄糖及其焦磷酸解作用。为了更清楚地了解大肠杆菌的葡萄糖-1-磷酸胸苷基转移酶的催化特性，特别是区分乒乓和顺序有序的bi bi反应机理，在不同底物和抑制剂存在下对酶的动力学特性进行了分析。此外，还存在三种不同的葡萄糖-1-磷酸胸苷基转移酶复合物（与dTDP共结晶，X射线晶体学分析了dTMP和d-葡萄糖1-葡萄糖，d-胸苷和1-葡萄糖葡萄糖的分离度，其分离度为1.9-2.3 A（R因子为17.3-17.5％）。同四聚酶在接近准罗斯曼折叠的拓扑转换点的表面腔中显示出高度保守的底物/抑制剂结合模式。对亚基三级结构的检查揭示了与核苷酸糖生物合成中涉及的其他酶的关系，包括远处
• Global probabilistic annotation of metabolic networks enables enzyme discovery
  作者：Germán Plata、Tobias Fuhrer、Tzu-Lin Hsiao、Uwe Sauer、Dennis Vitkup

  DOI：10.1038/nchembio.1063

  日期：2012.10

  A new global annotation strategy combines sequence identity and genomic context to provide probabilities for all metabolic assignments in a given species. Application of this method leads to multiple new annotations and validation of three enzymatic activities in B. subtilis. Annotation of organism-specific metabolic networks is one of the main challenges of systems biology. Importantly, owing to inherent uncertainty of computational annotations, predictions of biochemical function need to be treated probabilistically. We present a global probabilistic approach to annotate genome-scale metabolic networks that integrates sequence homology and context-based correlations under a single principled framework. The developed method for global biochemical reconstruction using sampling (GLOBUS) not only provides annotation probabilities for each functional assignment but also suggests likely alternative functions. GLOBUS is based on statistical Gibbs sampling of probable metabolic annotations and is able to make accurate functional assignments even in cases of remote sequence identity to known enzymes. We apply GLOBUS to genomes of Bacillus subtilis and Staphylococcus aureus and validate the method predictions by experimentally demonstrating the 6-phosphogluconolactonase activity of YkgB and the role of the Sps pathway for rhamnose biosynthesis in B. subtilis.

  一种新的全局注释策略结合了序列同一性和基因组上下文，为特定物种的所有代谢分配提供了概率。这种方法的应用带来了多种新的注释，并验证了枯草杆菌中的三种酶活性。 注释生物特异性代谢网络是系统生物学的主要挑战之一。重要的是，由于计算注释固有的不确定性，需要对生化功能的预测进行概率处理。我们提出了一种注释基因组尺度代谢网络的全局概率方法，它将序列同源性和基于上下文的相关性整合在一个单一的原则性框架下。所开发的利用采样进行全局生化重建的方法（GLOBUS）不仅为每个功能分配提供了注释概率，而且还提出了可能的替代功能。GLOBUS 基于对可能的代谢注释进行统计吉布斯采样，即使在与已知酶的序列同一性很低的情况下，也能进行准确的功能分配。我们将 GLOBUS 应用于枯草芽孢杆菌和金黄色葡萄球菌的基因组，并通过实验证明了 YkgB 的 6-phosphogluconolactonase 活性以及 Sps 途径在枯草芽孢杆菌鼠李糖生物合成中的作用，从而验证了该方法的预测结果。
• Mechanistic Evaluation of a Nucleoside Tetraphosphate with a Thymidylyltransferase
  作者：Stephanie M. Forget、Deborah A. Smithen、Alison Jee、David L. Jakeman

  DOI：10.1021/bi501438p

  日期：2015.3.3

  Pyrimidine polyphosphates were first detected in cells 5 decades ago; however, their biological significance remains only partially resolved. Such nucleoside polyphosphates are believed to be produced nonspecifically by promiscuous enzymes. Herein, synthetically prepared deoxythymidine 5'-tetraphosphate (p(4)dT) was evaluated with a thymidylyltransferase, Cps2L. We have identified p(4)dT as a substrate for Cps2L and evaluated the reaction pathway by analysis of products using high-performance liquid chromatography, liquid chromatography and tandem mass spectrometry, and P-31 nuclear magnetic resonance spectroscopy. Product analysis confirmed production of dTDP-Glc and triphosphate (P-3) and showed no trace of dTTP-Glc and PPi, which could arise from alternative pathways for the reaction mechanism.