Ribulose-5-phosphate | 551-85-9

• 分子结构分类: 有机化合物 - 有机氧化合物
• 英文名称: Ribulose-5-phosphate
• 英文别名: D-ribulose 5-phosphate；ru5p；[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl] dihydrogen phosphate
• CAS: 551-85-9；4151-19-3
• 化学式: C₅H₁₁O₈P
• 分子量: 230.111
• InChiKey: FNZLKVNUWIIPSJ-UHNVWZDZSA-N

物化性质

• 沸点：
  620.3±65.0 °C(Predicted)
• 密度：
  1.812±0.06 g/cm3(Predicted)
• 溶解度：
  可溶于甲醇（轻微）、水（轻微、超声处理）
• 物理描述：
  Solid
• 碰撞截面：
  148.8 Ų [M+Na]+ [CCS Type: DT, Method: single field calibrated with Agilent tune mix (Agilent)]

计算性质

• 辛醇/水分配系数(LogP)：
  -3.7
• 重原子数：
  14
• 可旋转键数：
  6
• 环数：
  0.0
• sp3杂化的碳原子比例：
  0.8
• 拓扑面积：
  145
• 氢给体数：
  5
• 氢受体数：
  8

反应信息

• 作为反应物：
  描述：

  Ribulose-5-phosphate 生成 [(2R)-2-羟基-3-氧代丁基]磷酸二氢酯
  参考文献：
  名称：

  VOLK, RAINER, FAK. CHEM., BIOL. UND GEOWISS. TESNN. UNIV. MUNSNEN, DOKT. NATURWISS. S19+

  摘要：

  DOI：
• 作为产物：
  描述：

  葡糖酸 在 6-phosphogluconic dehydrogenase 、 gluconate kinase 、 烟酰胺腺嘌呤双核苷酸磷酸盐 、 5’-三磷酸腺苷 、 magnesium chloride 作用下， 生成 Ribulose-5-phosphate
  参考文献：
  名称：

  Electrochemical oxidation of sugars at moderate potentials catalyzed by Rh porphyrins

  摘要：

  在这项研究中，我们证明了某些类型的铑卟啉在炭黑上能够在低电位下电化学氧化醛糖。其起始电位远低于其他基于络合物的催化剂。产品分析表明，该反应涉及醛基的2电子氧化。

  DOI：

  10.1039/c003026k
• 作为试剂：
  描述：

  L-色氨酸 在 Ribulose-5-phosphate 、 ambiguine I₁ homologues of isonitrile synthase A 、 ambiguine I₂ homologues of isonitrile synthase A 、 ambiguine I₃ homologues of isonitrile synthase B 、 2-氧代-戊二酸离子(2-) 、 铁粉 作用下， 生成 (Z)-3-(2-isocyanovinyl)-1H-indole
  参考文献：
  名称：

  蓝藻费氏小球藻中比比吲哚生物碱的生物合成

  摘要：

  Ambiguines属于哈巴吲哚型吲哚生物碱天然产物家族，许多成员在稠合的五环6-6-6-5-7环骨架中拥有多达八个连续的碳立体中心。在这里，我们报告鉴定了一个42 kbp的歧义素（amb）生物合成基因簇，该簇在其天然生产商Fischerella ambigua UTEX1903中包含32个蛋白质编码基因。该协会AMB与ambiguine生物合成簇通过两个生物信息学分析，并证实在体外（（ -负责3酶的表征ž）-2'- isocyanoethenyl）吲哚和焦磷酸香叶酯的生物合成和C-2的吲哚dimethylallyltransferase该区域专一调适内hapalindole g至ambiguine A.五非血红素铁依赖性加氧酶编码基因（包括4 Rieske型氧酶）的存在AMB簇表明，后期C–H活化可能是由于区域和立体特异性氯化，羟基化，环氧化和sp 2 –sp 3 C–C键形成而导致歧义素的结构多样性的原因。

  DOI：

  10.1021/cb400681n

文献信息

• Simultaneous Quantification of Metabolites Involved in Central Carbon and Energy Metabolism Using Reversed-Phase Liquid Chromatography−Mass Spectrometry and in Vitro ¹³C Labeling
  作者：Wen-Chu Yang、Miroslav Sedlak、Fred E. Regnier、Nathan Mosier、Nancy Ho、Jiri Adamec

  DOI：10.1021/ac801693c

  日期：2008.12.15

  Comprehensive analysis of intracellular metabolites is a critical component of elucidating cellular processes. Although the resolution and flexibility of reversed-phase liquid chromatography−mass spectrometry (RPLC−MS) makes it one of the most powerful analytical tools for metabolite analysis, the structural diversity of even the simplest metabolome provides a formidable analytical challenge. Here we describe a robust RPLC−MS method for identification and quantification of a diverse group of metabolites ranging from sugars, phosphosugars, and carboxylic acids to phosphocarboxylics acids, nucleotides, and coenzymes. This method is based on in vitro derivatization with a 13C-labeled tag that allows internal standard based quantification and enables separation of structural isomer pairs like glucose 6-phosphate and fructose 6-phosphate in a single chromatographic run. Calibration curves for individual metabolites showed linearity ranging over more than 2 orders of magnitude with correlation coefficients of R2 > 0.9975. The detection limits at a signal-to-noise ratio of 3 were below 1.0 μM (20 pmol) for most compounds. Thirty common metabolites involved in glycolysis, the pentose phosphate pathway, and tricarboxylic acid cycle were identified and quantified from yeast lysate with a relative standard deviation of less than 10%.

  详细分析细胞内代谢物是阐明细胞过程的关键组成部分。尽管反相液相色谱-质谱联用（RPLC-MS）的分辨率和灵活性使其成为代谢物分析中最强大的分析工具之一，但即使是简单的代谢组，其结构的多样性也带来了巨大的分析挑战。本文描述了一种稳健的RPLC-MS方法，用于鉴定和定量一系列广泛的代谢物，包括糖类、磷酸糖、羧酸、磷酸羧酸、核苷酸和辅酶。该方法基于使用13C标记标签的体外衍生化，允许基于内标的定量，并能在单次色谱运行中分离结构异构体对，如葡萄糖6-磷酸和果糖6-磷酸。单个代谢物的校准曲线显示线性范围超过两个数量级，相关系数R² > 0.9975。大多数化合物的信噪比为3的检测限低于1.0 μM（20 pmol）。从酵母裂解液中鉴定和定量了涉及糖酵解、戊糖磷酸途径和三羧酸循环的30种常见代谢物，相对标准偏差小于10%。
• Chemical Synthesis of Ketopentose-5-phosphates
  作者：Wei-Chih Wei、Che-Chien Chang

  DOI：10.1002/ejoc.201601639

  日期：2017.6.8

  The chemical synthesis of ketopentose-5-phosphates that are involved in the pentose phosphate pathway is developed. The ketopentose phosphates, D-ribulose-5-phosphate and D-xylulose-5-phosphate, were prepared in five steps starting from known intermediates. Starting from readily available D-aldopentoses, the reduction of the corresponding furanose derivatives gave key intermediates in the form of aldopentitols

  开发了参与磷酸戊糖途径的 5-磷酸酮戊糖的化学合成。磷酸酮戊糖、D-核酮糖-5-磷酸和D-木酮糖-5-磷酸是从已知中间体开始分五个步骤制备的。从容易获得的 D-戊醛糖开始，相应的呋喃糖衍生物的还原得到戊醛醇形式的关键中间体。选择性磷酸化、氧化，然后去保护提供目标分子。这种化学合成方法使这种磷酸酮糖很容易获得，这表明它们可以用作机理研究的测定底物。由于磷酸戊糖途径在癌细胞代谢中很重要，这种合成方法为制备用于药物开发的潜在酶抑制剂提供了机会。为了进一步扩展这种合成方法，以类似的方式在两种母体戊酮糖（D-核酮糖和 D-木酮糖）的合成中使用了不同的保护基团（三苯甲基）。
• Time-Dependent Profiling of Metabolites from Snf1 Mutant and Wild Type Yeast Cells
  作者：Elizabeth M. Humston、Kenneth M. Dombek、Jamin C. Hoggard、Elton T. Young、Robert E. Synovec

  DOI：10.1021/ac800998j

  日期：2008.11.1

  The effect of sampling time in the context of growth conditions on a dynamic metabolic system was investigated in order to assess to what extent a single sampling time may be sufficient for general application, as well as to determine if useful kinetic information could be obtained. A wild type yeast strain (W) was compared to a snf1Δ mutant yeast strain (S) grown in high-glucose medium (R) and in low-glucose medium containing ethanol (DR). Under these growth conditions, different metabolic pathways for utilizing the different carbon sources are expected to be active. Thus, changes in metabolite levels relating to the carbon source in the growth medium were anticipated. Furthermore, the Snf1 protein kinase complex is required to adapt cellular metabolism from fermentative R conditions to oxidative DR conditions. So, differences in intracellular metabolite levels between the W and S yeast strains were also anticipated. Cell extracts were collected at four time points (0.5, 2, 4, 6 h) after shifting half of the cells from R to DR conditions, resulting in 16 sample classes (WR, WDR, SR, SDR) × (0.5, 2, 4, 6 h). The experimental design provided time course data, so temporal dependencies could be monitored in addition to carbon source and strain dependencies. Comprehensive two-dimensional (2D) gas chromatography coupled to time-of-flight mass spectrometry (GC × GC-TOFMS) was used with discovery-based data mining algorithms (Anal. Chem. 2006, 78, 5068–5075 (ref 1); J. Chromatogr., A 2008, 1186, 401–411 (ref 2)) to locate regions within the 2D chromatograms (i.e., metabolites) that provided chemical selectivity between the 16 sample classes. These regions were mathematically resolved using parallel factor analysis to positively identify the metabolites and to acquire quantitative results. With these tools, 51 unique metabolites were identified and quantified. Various time course patterns emerged from these data, and principal component analysis (PCA) was utilized as a comparison tool to determine the sources of variance between these 51 metabolites. The effect of sampling time was investigated with separate PCA analyses using various subsets of the data. PCA utilizing all of the time course data, averaged time course data, and each individual time point data set independently were performed to discern the differences. For the yeast strains examined in the current study, data collection at either 4 or 6 h provided information comparable to averaged time course data, albeit with a few metabolites missing using a single sampling time point.

  在动态代谢系统的背景下，研究了采样时间在生长条件下的影响，以评估在一般应用中单一采样时间可能足够到何种程度，以及是否可以获得有用的动力学信息。将野生型酵母菌株（W）与snf1Δ突变型酵母菌株（S）在高葡萄糖培养基（R）和含乙醇的低葡萄糖培养基（DR）中进行比较。在这些生长条件下，预计会激活利用不同碳源的不同代谢途径，因此预期与生长培养基中碳源相关的代谢物水平会发生变化。此外，Snf1蛋白激酶复合体是适应细胞代谢从发酵R条件到氧化DR条件所必需的，因此也预期W和S酵母菌株之间的胞内代谢物水平存在差异。在将一半细胞从R条件转移到DR条件后的四个时间点（0.5、2、4、6小时）收集细胞提取物，产生了16个样本类别（WR、WDR、SR、SDR）×（0.5、2、4、6小时）。实验设计提供了时间进程数据，因此除了碳源和菌株依赖性外，还可以监测时间依赖性。综合二维（2D）气相色谱与飞行时间质谱（GC×GC-TOFMS）结合基于发现的挖掘算法（《分析化学》2006，78，5068–5075（参考文献1）；《色谱A》2008，1186，401–411（参考文献2））用于在2D色谱图中定位在16个样本类别之间提供化学选择性的区域（即代谢物）。这些区域通过平行因子分析进行数学解析，以正向鉴定代谢物并获取定量结果。利用这些工具，识别并定量了51种独特代谢物。这些数据中出现了各种时间进程模式，并利用主成分分析（PCA）作为比较工具来确定这51种代谢物之间的变异来源。通过使用数据的不同子集进行单独的PCA分析，研究了采样时间的影响。利用所有时间进程数据、平均时间进程数据以及每个独立时间点数据集分别进行了PCA分析，以辨别差异。对于当前研究中考察的酵母菌株，在4或6小时收集数据提供的信息与平均时间进程数据相当，尽管使用单一采样时间点时会缺失一些代谢物。
• Biocatalysts from cyanobacterial hapalindole pathway afford antivirulent isonitriles against MRSA
  作者：Brittney M Bunn、Mizhi Xu、Chase M Webb、Rajesh Viswanathan

  DOI：10.1007/s12038-021-00156-4

  日期：2021.6

  The emergence of resistance to frontline antibiotics has called for novel strategies to combat serious pathogenic infections. Methicillin-resistant Staphylococcus aureus [MRSA] is one such pathogen. As opposed to traditional antibiotics, bacteriostatic anti-virulent agents disarm MRSA, without exerting pressure, that cause resistance. Herein, we employed a thermophilic Thermotoga maritima tryptophan synthase (TmTrpB1) enzyme followed by an isonitrile synthase and Fe(II)-α-ketoglutarate-dependent oxygenase, in sequence as biocatalysts to produce antivirulent indole vinyl isonitriles. We report on conversion of simple derivatives of indoles to their C3-vinyl isonitriles, as the enzymes employed here demonstrated broader substrate tolerance. In toto, eight distinct L-Tryptophan derived α-amino acids (7) were converted to their bioactive vinyl isonitriles (3) by action of an isonitrile synthase (WelI1) and an Fe(II)-α-ketoglutarate-dependent oxygenase (WelI3) yielding structural variants possessing antivirulence against MRSA. These indole vinyl isonitriles at 10 μg/mL are effective as antivirulent compounds against MRSA, as evidenced through analysis of rabbit blood hemolysis assay. Based on a homology modelling exercise, of enzyme-substrate complexes, we deduced potential three dimensional alignments of active sites and glean mechanistic insights into the substrate tolerance of the Fe(II)-α-ketoglutarate-dependent oxygenase.

  一线抗生素耐药性的出现，要求我们采取新的策略来应对严重的病原体感染。耐甲氧西林金黄色葡萄球菌（MRSA）就是这样一种病原体。与传统抗生素相比，抑菌性抗病毒制剂能解除 MRSA 的威胁，而不会对其造成压力，导致其产生耐药性。在此，我们采用了嗜热的海洋嗜热菌（Thermotoga maritima）色氨酸合成酶（TmTrpB1）、异腈合成酶和依赖于Fe(II)-α-酮戊二酸的加氧酶作为生物催化剂，依次生成抗病毒的吲哚乙烯基异腈。我们报告了将吲哚的简单衍生物转化为其 C3-乙烯基异腈的情况，因为这里使用的酶具有更广泛的底物耐受性。在异腈合成酶（WelI1）和依赖于Fe（II）-α-酮戊二酸的加氧酶（WelI3）的作用下，总共有八种不同的L-色氨酸衍生的α-氨基酸（7）被转化为具有生物活性的乙烯基异腈（3），产生的结构变体对MRSA具有抗病毒作用。这些吲哚乙烯基异腈类化合物在 10 μg/mL 的浓度下可作为抗 MRSA 的有效抗病毒化合物，兔血液溶血试验分析证明了这一点。基于酶-底物复合物的同源建模工作，我们推导出了活性位点的潜在三维排列，并从机理上深入了解了依赖铁（II）-α-酮戊二酸的加氧酶对底物的耐受性。
• In Vitro Stepwise Reconstitution of Amino Acid Derived Vinyl Isocyanide Biosynthesis: Detection of an Elusive Intermediate
  作者：Wei-chen Chang、Dev Sanyal、Jhih-Liang Huang、Kuljira Ittiamornkul、Qin Zhu、Xinyu Liu

  DOI：10.1021/acs.orglett.7b00258

  日期：2017.3.3

  and AmbI2) and the detection of an elusive intermediate (S)-3-(1H-indol-3-yl)-2-isocyanopropanoic acid 1 in indolyl vinyl isocyanide biogenesis are reported. The characterization of iron/2-oxoglutarate (Fe/2OG) dependent desaturases IsnB and AmbI3 sheds light on the possible mechanism underlying stereoselective alkene installation to complete the biosynthesis of (E)- and (Z)-3-(2-isocyanovinyl)-1H-indole

  报道了新发现的异腈合酶（AmbI1和AmbI2）的体外重构以及在吲哚基乙烯基异氰酸酯生物发生中难以捉摸的中间体（S）-3-（1 H-吲哚-3-基）-2-异氰基丙酸1的检测。铁/ 2-氧戊二酸（Fe / 2OG）依赖的去饱和酶IsnB和AmbI3的表征揭示了立体选择性烯烃安装以完成（E）-和（Z）-3-（2-异氰基乙烯基）-的生物合成的可能机制。 1 H-吲哚2和5。易处理的异腈合酶系统（AmbI1和AmbI2）的建立为阐明神秘的异氰酸酯形成酶机制铺平了道路。