S-[2-[3-[[4-[[[(2R,3S,4R,5R)-5-(6-氨基嘌呤-9-基)-4-羟基-3-膦酰氧基四氢呋喃-2-基]甲氧基-羟基磷酰]氧基-羟基磷酰]氧基-2-羟基-3,3-二甲基丁酰基]氨基]丙酰氨基]乙基]甲烷硫酸酯 | 13131-49-2

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘌呤核苷酸
• 中文名称: S-[2-[3-[[4-[[[(2R,3S,4R,5R)-5-(6-氨基嘌呤-9-基)-4-羟基-3-膦酰氧基四氢呋喃-2-基]甲氧基-羟基磷酰]氧基-羟基磷酰]氧基-2-羟基-3,3-二甲基丁酰基]氨基]丙酰氨基]乙基]甲烷硫酸酯
• 英文名称: formyl CoA
• 英文别名: formyl-CoA；S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutanoyl]amino]propanoylamino]ethyl] methanethioate
• CAS: 13131-49-2
• 化学式: C₂₂H₃₆N₇O₁₇P₃S
• 分子量: 795.552
• InChiKey: SXMOKYXNAPLNCW-GORZOVPNSA-N

计算性质

• 辛醇/水分配系数(LogP)：
  -5.6
• 重原子数：
  50
• 可旋转键数：
  20
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.64
• 拓扑面积：
  389
• 氢给体数：
  9
• 氢受体数：
  22

反应信息

• 作为反应物：
  描述：

  琥珀半醛 、 S-[2-[3-[[4-[[[(2R,3S,4R,5R)-5-(6-氨基嘌呤-9-基)-4-羟基-3-膦酰氧基四氢呋喃-2-基]甲氧基-羟基磷酰]氧基-羟基磷酰]氧基-2-羟基-3,3-二甲基丁酰基]氨基]丙酰氨基]乙基]甲烷硫酸酯 在 human 2-hydroxyacyl Coenzyme A lyase 、 焦磷酸硫胺素 、 magnesium chloride 作用下， 以 aq. buffer 为溶剂， 反应 1.0h， 生成 2-hydroxy-glutaryl-CoA
  参考文献：
  名称：

  草酰辅酶 A 脱羧酶能够将醛亲核一碳延伸成手性 α-羟基酸。

  摘要：

  从简单的、可再生的碳单元合成复杂的分子是可持续经济的目标。在这里，我们探索了硫胺素二磷酸依赖性（ThDP）草酰辅酶A脱羧酶（OXC）/2-羟酰辅酶A裂解酶（HACL）超家族的生物催化潜力，该家族通过释放C1-单位甲酰辅酶A。我们表明 OXC/HACL 超家族包含混杂的成员，这些成员可以逆转以进行各种醛的亲核 C1 延伸，产生相应的 2-羟基酰基-CoA 硫酯。我们通过合理的酶工程改进了 Mmethylorubrum extorquens OXC 的催化性能，并将其与两种新描述的酶（特定的草酰辅酶 A 合成酶和 2-羟酰辅酶 A 硫酯酶）相结合。这种酶级联能够将草酸盐和芳香醛连续转化为有价值的 (S)-α-羟基酸，对映体过量高达 99%。

  DOI：

  10.1002/anie.201915155
• 作为产物：
  描述：

  oxalyl coenzyme A 在 oxalyl CoA decarboxylase from Escherichia coli strain BL₂₁ 、 焦磷酸硫胺素 、 magnesium sulfate 作用下， 生成 S-[2-[3-[[4-[[[(2R,3S,4R,5R)-5-(6-氨基嘌呤-9-基)-4-羟基-3-膦酰氧基四氢呋喃-2-基]甲氧基-羟基磷酰]氧基-羟基磷酰]氧基-2-羟基-3,3-二甲基丁酰基]氨基]丙酰氨基]乙基]甲烷硫酸酯
  参考文献：
  名称：

  New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli

  摘要：

  The gene yfdU from Escherichia coli encodes a putative oxalyl coenzyme A decarboxylase, a thiamine diphosphate‐dependent enzyme that is potentially involved in the degradation of oxalate. The enzyme has been purified to homogeneity. The kinetic constants for conversion of the substrate oxalyl coenzyme A by the enzyme in the absence and presence of the inhibitor coenzyme A, as well as in the absence and presence of the activator adenosine 5′‐diphosphate, were determined using a novel continuous optical assay. The effects of these ligands on the solution and crystal structure of the enzyme were studied using small‐angle X‐ray scattering and X‐ray crystal diffraction. Analyses of the obtained crystal structures of the enzyme in complex with the cofactor thiamine diphosphate, the activator adenosine 5′‐diphosphate and the inhibitor acetyl coenzyme A, as well as the corresponding solution scattering patterns, allow comparison of the oligomer structures of the enzyme complexes under various experimental conditions, and provide insights into the architecture of substrate and effector binding sites.Structured digital abstract MINT‐7717846: EcODC (uniprotkb:P0AFI0) and EcODC (uniprotkb:P0AFI0) bind (MI:0407) by X‐ray scattering (MI:0826) MINT‐7717834: EcODC (uniprotkb:P0AFI0) and EcODC (uniprotkb:P0AFI0) bind (MI:0407) by X‐ray crystallography (MI:0114)

  DOI：

  10.1111/j.1742-4658.2010.07673.x

文献信息

• Metal-free organocatalytic S-formylation of thiols using CO2
  作者：Subir Maji、Arpan Das、Madhur Mahesh Bhatt、Swadhin K. Mandal

  DOI：10.1038/s41929-024-01114-7

  日期：——

  anti-inflammatory medication molecules, as well as preparation of 13C-labelled formyl coenzyme A. Furthermore, we establish a one-pot S-formylation-olefination process for the synthesis of vinyl sulfides under completely metal-free conditions in the presence of CO2. Overall, this study provides a platform to transform thiols and CO2 into value-added products.

  硫醇的S-甲酰化是通过甲酸脱氢酶催化的酶促过程实现的，该酶将CO 2固定在底物上，这在调节活生物体的重要生物途径中起着至关重要的作用。通过化学方法实现这种反应性也可能是有利的，这将允许将CO 2固定在多种硫醇上。在这里，我们演示了在无金属条件下使用介离子N-杂环烯烃从CO 2制备S-甲酰硫醇的化学过程。该催化反应用于多样化从天然萜类化合物、脂肪醇、抗氧化剂和市售镇痛抗炎药物分子中获得的多种生物活性硫醇，以及13 C 标记的甲酰辅酶 A 的制备。此外，我们建立了在CO 2存在下完全无金属条件下合成乙烯基硫醚的一锅S-甲酰化-烯化工艺。总的来说，这项研究提供了一个将硫醇和CO 2转化为增值产品的平台。
• Crystal Structures of <i>Acetobacter aceti</i> Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase Reveal Specificity Determinants and Illustrate the Mechanism Used by Class I CoA-Transferases
  作者：Elwood A. Mullins、T. Joseph Kappock

  DOI：10.1021/bi300957f

  日期：2012.10.23

  Coenzyme A (CoA)-transferases catalyze transthioesterification reactions involving acyl-CoA substrates, using an active-site carboxylate to form covalent acyl anhydride and CoA thioester adducts. Mechanistic studies of class I CoA-transferases suggested that acyl-CoA binding energy is used to accelerate rate-limiting acyl transfers by compressing the substrate thioester tightly against the catalytic glutamate [White, H., and Jencks, W. P. (1976) J. Biol. Chem. 251, 1688-1699]. The class I CoA-transferase succinyl-CoA:acetate CoA-transferase is an acetic acid resistance factor (AarC) with a role in a variant citric acid cycle in Acetobacter aceti. In an effort to identify residues involved in substrate recognition, X-ray crystal structures of a C-terminally His(6)-tagged form (AarCH6) were determined for several wild-type and mutant complexes, including freeze trapped acetylglutamyl anhydride and glutamyl-CoA thioester adducts. The latter shows the acetate product bound to an auxiliary site that is required for efficient carboxylate substrate recognition. A mutant in which the catalytic glutamate was changed to an alanine crystallized in a closed complex containing dethiaacetyl-CoA, which adopts an unusual curled conformation. A model of the acetyl-CoA Michaelis complex demonstrates the compression anticipated four decades ago by Jencks and reveals that the nucleophilic glutamate is held at a near-ideal angle for attack as the thioester oxygen is forced into an oxyanion hole composed of Gly388 NH and CoA N2 ''. CoA is nearly immobile along its entire length during all stages of the enzyme reaction. Spatial and sequence conservation of key residues indicates that this mechanism is general among class I CoA-transferases.
• Oxalyl‐CoA Decarboxylase Enables Nucleophilic One‐Carbon Extension of Aldehydes to Chiral α‐Hydroxy Acids
  作者：Simon Burgener、Niña Socorro Cortina、Tobias J. Erb

  DOI：10.1002/anie.201915155

  日期：2020.3.27

  be reversed to perform nucleophilic C1 -extensions of various aldehydes to yield the corresponding 2-hydroxyacyl-CoA thioesters. We improved the catalytic properties of Methylorubrum extorquens OXC by rational enzyme engineering and combined it with two newly described enzymes-a specific oxalyl-CoA synthetase and a 2-hydroxyacyl-CoA thioesterase. This enzymatic cascade enabled continuous conversion

  从简单的、可再生的碳单元合成复杂的分子是可持续经济的目标。在这里，我们探索了硫胺素二磷酸依赖性（ThDP）草酰辅酶A脱羧酶（OXC）/2-羟酰辅酶A裂解酶（HACL）超家族的生物催化潜力，该家族通过释放C1-单位甲酰辅酶A。我们表明 OXC/HACL 超家族包含混杂的成员，这些成员可以逆转以进行各种醛的亲核 C1 延伸，产生相应的 2-羟基酰基-CoA 硫酯。我们通过合理的酶工程改进了 Mmethylorubrum extorquens OXC 的催化性能，并将其与两种新描述的酶（特定的草酰辅酶 A 合成酶和 2-羟酰辅酶 A 硫酯酶）相结合。这种酶级联能够将草酸盐和芳香醛连续转化为有价值的 (S)-α-羟基酸，对映体过量高达 99%。
• New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli
  作者：Tobias Werther、Agnes Zimmer、Georg Wille、Ralph Golbik、Manfred S. Weiss、Stephan König

  DOI：10.1111/j.1742-4658.2010.07673.x

  日期：2010.6

  The gene yfdU from Escherichia coli encodes a putative oxalyl coenzyme A decarboxylase, a thiamine diphosphate‐dependent enzyme that is potentially involved in the degradation of oxalate. The enzyme has been purified to homogeneity. The kinetic constants for conversion of the substrate oxalyl coenzyme A by the enzyme in the absence and presence of the inhibitor coenzyme A, as well as in the absence and presence of the activator adenosine 5′‐diphosphate, were determined using a novel continuous optical assay. The effects of these ligands on the solution and crystal structure of the enzyme were studied using small‐angle X‐ray scattering and X‐ray crystal diffraction. Analyses of the obtained crystal structures of the enzyme in complex with the cofactor thiamine diphosphate, the activator adenosine 5′‐diphosphate and the inhibitor acetyl coenzyme A, as well as the corresponding solution scattering patterns, allow comparison of the oligomer structures of the enzyme complexes under various experimental conditions, and provide insights into the architecture of substrate and effector binding sites.Structured digital abstract MINT‐7717846: EcODC (uniprotkb:P0AFI0) and EcODC (uniprotkb:P0AFI0) bind (MI:0407) by X‐ray scattering (MI:0826) MINT‐7717834: EcODC (uniprotkb:P0AFI0) and EcODC (uniprotkb:P0AFI0) bind (MI:0407) by X‐ray crystallography (MI:0114)