S-methyl-1-thio-D-xylulose 5-phosphate

• 分子结构分类: 有机化合物 - 有机氧化合物
• 英文名称: S-methyl-1-thio-D-xylulose 5-phosphate
• 英文别名: [(2R,3S)-2,3-dihydroxy-5-methylsulfanyl-4-oxopentyl] phosphate
• 化学式: C6H11O7PS-2
• 分子量: 258.19
• InChiKey: JQZPXWYLEQDBGH-XINAWCOVSA-L

计算性质

• 辛醇/水分配系数(LogP)：
  -2.6
• 重原子数：
  15
• 可旋转键数：
  6
• 环数：
  0.0
• sp3杂化的碳原子比例：
  0.83
• 拓扑面积：
  155
• 氢给体数：
  2
• 氢受体数：
  8

反应信息

• 作为反应物：
  描述：

  (R)-2-((S)-4-Amino-4-carboxy-butyrylamino)-2-(carboxymethyl-carbamoyl)-ethanethiol anion 、 S-methyl-1-thio-D-xylulose 5-phosphate 生成 1-deoxy-D-xylulose 5-phosphate 、 S-(methylsulfanyl)glutathione
  参考文献：
  名称：

  A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis

  摘要：

  结合全息技术（omics），确定了参与连接多胺代谢与异戊烯生物合成的新蛋氨酸挽救途径的四种酶的功能。这一反应序列涉及自然界最丰富的蛋白质--二氧化碳固定酶 RubisCO 的同源物。 在大规模基因组测序时代，未定性蛋白质的功能分配是一项挑战。在这里，我们将提取物核磁共振、蛋白质组学和转录物组学与新开发的（基因敲除）代谢组学平台结合起来，确定了一种来自红霉的核酮糖-1,5-二磷酸羧化酶/氧合酶（RubisCO）类蛋白的潜在生理作用。我们的研究揭示了细菌中心碳代谢中依赖于S-腺苷蛋氨酸的多胺代谢与异戊烯类生物合成之间意想不到的联系，同时也为在有机体水平上确定酶的功能提供了另一种方法。

  DOI：

  10.1038/nchembio.1087
• 作为产物：
  描述：

  S-methyl-5-thio-D-ribulose 1-phosphate(2-) 生成 S-methyl-1-thio-D-xylulose 5-phosphate
  参考文献：
  名称：

  A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis

  摘要：

  结合全息技术（omics），确定了参与连接多胺代谢与异戊烯生物合成的新蛋氨酸挽救途径的四种酶的功能。这一反应序列涉及自然界最丰富的蛋白质--二氧化碳固定酶 RubisCO 的同源物。 在大规模基因组测序时代，未定性蛋白质的功能分配是一项挑战。在这里，我们将提取物核磁共振、蛋白质组学和转录物组学与新开发的（基因敲除）代谢组学平台结合起来，确定了一种来自红霉的核酮糖-1,5-二磷酸羧化酶/氧合酶（RubisCO）类蛋白的潜在生理作用。我们的研究揭示了细菌中心碳代谢中依赖于S-腺苷蛋氨酸的多胺代谢与异戊烯类生物合成之间意想不到的联系，同时也为在有机体水平上确定酶的功能提供了另一种方法。

  DOI：

  10.1038/nchembio.1087

文献信息

• Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris
  作者：Anthony R. Miller、Justin A. North、John A. Wildenthal、F. Robert Tabita

  DOI：10.1128/mbio.00407-18

  日期：2018.5.2

  in the presence of oxygen, to salvage sulfur, R. palustris employs two pathways, both of which result in production of volatile methanethiol, a key compound of the global sulfur cycle. When total available sulfur was plentiful, methanethiol was readily released into the environment. However, when sulfur became limiting, methanethiol release decreased, presumably due to methanethiol utilization to regenerate

  5'-甲基硫腺苷 (MTA) 是一种死端的含硫代谢物和细胞抑制剂，由 S-腺苷-l-甲硫氨酸依赖性反应产生。最近的研究表明，有多种细菌甲硫氨酸回收途径 (MSP) 可用于 MTA 解毒和硫回收。在这里，通过结合基因缺失和定向代谢物检测研究，我们报告说，在有氧条件下，兼性厌氧细菌沼泽红假单胞菌采用与先前在红色红螺菌中描述的相同的 MTA-类异戊二烯分流器和第二种新型 MSP，两者均生成甲硫醇中间体。额外的 R. palustris 好氧 MSP，一种二羟基丙酮磷酸盐 (DHAP)-甲硫醇分流器，最初将 MTA 转化为 2-(甲硫基) 乙醇和 DHAP。这与最近报道的厌氧乙烯形成 MSP（DHAP-乙烯分流器）的初始步骤相同。有氧 DHAP-甲硫醇分流然后进一步将 2-(甲硫基)乙醇代谢为甲硫醇，其可被 O-乙酰基-1-高丝氨酸硫化氢化酶直接利用以再生甲硫氨酸。这与厌氧 DHAP-乙烯分流相反，后者将
• Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways
  作者：Kyuil Cho、Bradley S. Evans、B. McKay Wood、Ritesh Kumar、Tobias J. Erb、Benjamin P. Warlick、John A. Gerlt、Jonathan V. Sweedler

  DOI：10.1007/s11306-014-0713-3

  日期：2015.6

  While recent advances in metabolomic measurement technologies have been dramatic, extracting biological insight from complex metabolite profiles remains a challenge. We present an analytical strategy that uses data obtained from high resolution liquid chromatography–mass spectrometry and a bioinformatics toolset for detecting actively changing metabolic pathways upon external perturbation. We begin with untargeted metabolite profiling to nominate altered metabolites and identify pathway candidates, followed by validation of those pathways with transcriptomics. Using the model organisms Rhodospirillum rubrum and Bacillus subtilis, our results reveal metabolic pathways that are interconnected with methionine salvage. The rubrum-type methionine salvage pathway is interconnected with the active methyl cycle in which re-methylation, a key reaction for recycling methionine from homocysteine, is unexpectedly suppressed; instead, homocysteine is catabolized by the trans-sulfuration pathway. Notably, the non-mevalonate pathway is repressed, whereas the rubrum-type methionine salvage pathway contributes to isoprenoid biosynthesis upon 5′-methylthioadenosine feeding. In this process, glutathione functions as a coenzyme in vivo when 1-methylthio-d-xylulose 5-phosphate (MTXu 5-P) methylsulfurylase catalyzes dethiomethylation of MTXu 5-P. These results clearly show that our analytical approach enables unexpected metabolic pathways to be uncovered.

  虽然近年来代谢组学测量技术取得了巨大进步，但从复杂的代谢物图谱中提取生物信息仍是一项挑战。我们提出了一种分析策略，利用从高分辨率液相色谱-质谱联用仪获得的数据和生物信息学工具集，检测在外部扰动下发生积极变化的代谢途径。我们首先通过非靶向代谢物分析来确定发生变化的代谢物并确定候选通路，然后通过转录组学对这些通路进行验证。利用模式生物红柱菌（Rhodospirillum rubrum）和枯草芽孢杆菌（Bacillus subtilis），我们的研究结果揭示了与蛋氨酸挽救相互关联的代谢途径。红球菌型蛋氨酸挽救途径与活跃的甲基循环相互关联，其中从同半胱氨酸回收蛋氨酸的关键反应--再甲基化--意外地被抑制；相反，同半胱氨酸通过反式硫化途径被分解。值得注意的是，非甲羟戊酸途径受到抑制，而红宝石型甲硫氨酸挽救途径在摄入 5′-甲硫基腺苷后有助于异戊二烯的生物合成。在这一过程中，当 1-甲硫基-d-木酮糖-5-磷酸（MTXu 5-P）甲基硫化酶催化 MTXu 5-P 的脱硫化作用时，谷胱甘肽在体内作为辅酶发挥作用。这些结果清楚地表明，我们的分析方法能够发现意想不到的代谢途径。
• Mechanistic Diversity in the RuBisCO Superfamily: A Novel Isomerization Reaction Catalyzed by the RuBisCO-like Protein from <i>Rhodospirillum rubrum</i>
  作者：Heidi J. Imker、Jaya Singh、Benjamin P. Warlick、F. Robert Tabita、John A. Gerlt

  DOI：10.1021/bi801685f

  日期：2008.10.28

  Some homologues of D-ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) do not catalyze carboxylation and are designated RuBisCO-like proteins (RLPs). The RLP from Rhodospirillunt rubrum (gi: 83593333) catalyzes a novel isomerization reaction (overall 1,3-proton transfer reaction; likely, two 1,2-proton transfer reactions) that converts 5-methylthio-D-ribulose 1-phosphate to a 3:1 mixture of 1-methylthioxylulose 5-phosphate and 1-methylthioribulose 5-phosphate. Disruption of the gene encoding the RLP abolishes the ability of R. rubrum to utilize 5'-methylthioadenosine as a sole sulfur source, implicating a new, as-yet-uncharacterized, pathway for sulfur salvage.
• A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis
  作者：Tobias J Erb、Bradley S Evans、Kyuil Cho、Benjamin P Warlick、Jaya Sriram、B McKay Wood、Heidi J Imker、Jonathan V Sweedler、F Robert Tabita、John A Gerlt

  DOI：10.1038/nchembio.1087

  日期：2012.11

  Combined omics techniques lead to the functional assignment of four enzymes involved in a new methionine salvage pathway linking polyamine metabolism with isoprenoid biosynthesis. This reaction sequence involves a homolog of nature's most abundant protein, the CO2-fixing enzyme RubisCO. Functional assignment of uncharacterized proteins is a challenge in the era of large-scale genome sequencing. Here, we combine in extracto NMR, proteomics and transcriptomics with a newly developed (knock-out) metabolomics platform to determine a potential physiological role for a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Rhodospirillum rubrum. Our studies unraveled an unexpected link in bacterial central carbon metabolism between S-adenosylmethionine–dependent polyamine metabolism and isoprenoid biosynthesis and also provide an alternative approach to assign enzyme function at the organismic level.

  结合全息技术（omics），确定了参与连接多胺代谢与异戊烯生物合成的新蛋氨酸挽救途径的四种酶的功能。这一反应序列涉及自然界最丰富的蛋白质--二氧化碳固定酶 RubisCO 的同源物。 在大规模基因组测序时代，未定性蛋白质的功能分配是一项挑战。在这里，我们将提取物核磁共振、蛋白质组学和转录物组学与新开发的（基因敲除）代谢组学平台结合起来，确定了一种来自红霉的核酮糖-1,5-二磷酸羧化酶/氧合酶（RubisCO）类蛋白的潜在生理作用。我们的研究揭示了细菌中心碳代谢中依赖于S-腺苷蛋氨酸的多胺代谢与异戊烯类生物合成之间意想不到的联系，同时也为在有机体水平上确定酶的功能提供了另一种方法。