2-氧代丁二酸 | 149-63-3

• 分子结构分类: 有机化合物 - 有机酸及其衍生物 - 酮酸及其衍生物
• 中文名称: 2-氧代丁二酸
• 中文别名: 2-羰基丁二酸
• 英文名称: oxaloacetate
• 英文别名: oxalacetate；2-oxobutanedioate
• CAS: 149-63-3
• 化学式: C₄H₂O₅
• 分子量: 130.057
• InChiKey: KHPXUQMNIQBQEV-UHFFFAOYSA-L

计算性质

• 辛醇/水分配系数(LogP)：
  0.7
• 重原子数：
  9
• 可旋转键数：
  1
• 环数：
  0.0
• sp3杂化的碳原子比例：
  0.25
• 拓扑面积：
  97.3
• 氢给体数：
  0
• 氢受体数：
  5

反应信息

• 作为反应物：
  描述：

  2-氧代丁二酸 在 pyruvate kinase 、 recombinant rat cytosolic phosphoenolpyruvate carboxykinase 、 二磷酸腺苷 、 Guanosine 5'-triphosphate 、 还原型辅酶Ⅰ 、 magnesium chloride 、 manganese(ll) chloride 、 L-lactate dehydrogenase 、 1,4-二巯基-2,3-丁二醇 作用下， 以 水 为溶剂， 生成 phosphoenolpyruvate
  参考文献：
  名称：

  Increasing the Conformational Entropy of the Ω-Loop Lid Domain in Phosphoenolpyruvate Carboxykinase Impairs Catalysis and Decreases Catalytic Fidelity,

  摘要：

  Many studies have shown that the dynamic motions of individual protein segments can play an important role in enzyme function. Recent structural studies of the gluconeogenic enzyme phosphoenolpyruvate carboxykinase (PEPCK) demonstrate that PEPCK contains a 10-residue Omega-loop domain that acts as an active site lid. On the basis of these structural studies, we have previously proposed a model for the mechanism of PEPCK catalysis in which the conformation of this mobile lid domain is energetically coupled to ligand binding, resulting in the closed conformation of the lid, necessary for correct substrate positioning, becoming more energetically favorable as ligands associate with the enzyme. Here we test this model by introducing a point mutation (A467G) into the center of the Omega-loop lid that is designed to increase the entropic penalty for lid closure. Structural and kinetic characterization of this mutant enzyme demonstrates that the mutation has decreased the favorability of the enzyme adapting the closed lid conformation. As a consequence of this shift in the equilibrium defining the conformation of the active site lid, the enzyme's ability to stabilize the reaction intermediate is weakened, resulting in catalytic defect. This stabilization is initially surprising, as the lid domain makes no direct contacts with the etiolate intermediate formed during the reaction. Furthermore, during the conversion of OAA to PEP, the destabilization of the lid-closed conformation results in the reaction becoming decoupled as the etiolate intermediate is protonated rather than phosphorylated, resulting in the formation of pyruvate. Taken together, the structural and kinetic characterization of A467G-PEPCK supports our model of the role of the active site lid in catalytic function and demonstrates that the shift in the lowest-energy conformation between open and closed lid states is a function of the free energy available to the enzyme through ligand binding and the entropic penalty for ordering of the 10-residue Omega-loop lid domain.

  DOI：

  10.1021/bi100399e
• 作为产物：
  描述：

  L-malate 在 还原型辅酶Ⅰ 、 malate dehydrogenase 作用下， 生成 2-氧代丁二酸
  参考文献：
  名称：

  Identification of Fumarate Hydratase Inhibitors with Nutrient-Dependent Cytotoxicity

  摘要：

  Development of cell-permeable small molecules that target enzymes involved in energy metabolism remains important yet challenging. We describe here the discovery of a new class of compounds with a nutrient-dependent cytotoxicity profile that arises from pharmacological inhibition of fumarate hydratase (also known as fumarase). This finding was enabled by a high-throughput screen of a diverse chemical library in a panel of human cancer cell lines cultured under different growth conditions, followed by subsequent structure-activity optimization and target identification. While the highest cytotoxicity was observed under low glucose concentrations, the antiproliferative activities and inhibition of oxygen consumption rates in cells were distinctly different from those displayed by typical inhibitors of mitochondrial oxidative phosphorylation. The use of a photoaffinity labeling strategy identified fumarate hydratase as the principal pharmacological target. Final biochemical studies confirmed dose-dependent, competitive inhibition of this enzyme in vitro, which was fully consistent with the initially observed growth inhibitory activity. Our work demonstrates how the phenotypic observations combined with a successful target identification strategy can yield a useful class of pharmacological inhibitors of an enzyme involved in the operation of tricarboxylic acid cycle.

  DOI：

  10.1021/ja5101257
• 作为试剂：
  描述：

  D-天门冬氨酸 在 磷酸吡哆醛 、 2-氧代丁二酸 、 sodium tartrate 、 aspartate racemase 作用下， 以 aq. phosphate buffer 为溶剂， 生成 L-天门冬氨酸
  参考文献：
  名称：

  A newly identified enzyme from Japanese common squid Todarodes pacificus has the ability to biosynthesize d-aspartate

  摘要：

  DOI：

  10.1016/j.abb.2023.109809

文献信息

• Effects of Gln102Arg and Cys97Gly mutations on the structural specificity and stereospecificity of the L-lactate dehydrogenase from Bacillus stearothermophilus
  作者：Helmut K. W. Kallwass、Marcel A. Luyten、Wendy Parris、Marvin Gold、Cyril M. Kay、J. Bryan Jones

  DOI：10.1021/ja00038a016

  日期：1992.6

  The L-lactate dehydrogenase of Bacillus stearothermophilus (BSLDH) is a thermostable enzyme with considerable potential for applications in asymmetric synthesis. An understanding of the factors controlling its structural specificity and stereospecificity is therefore of interest. In this paper the effects of GIn 102→Arg and Cys97→Gly mutations have been evaluated. In a survey of thirteen 2-keto acids

  嗜热脂肪芽孢杆菌 (BSLDH) 的 L-乳酸脱氢酶是一种热稳定酶，在不对称合成中具有相当大的应用潜力。因此，了解控制其结构特异性和立体特异性的因素是很有意义的。本文评估了 GIn 102→Arg 和 Cys97→Gly 突变的影响。在对 13 种 2-酮酸的调查中，发现 Q102R 突变降低了 BSLDH 还原具有小或亲水 R 基团的 RCOCOOH 底物的活性，而不影响其对具有较大疏水性 R 取代基的那些的活性
• L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH
  作者：Andrew M Intlekofer、Bo Wang、Hui Liu、Hardik Shah、Carlos Carmona-Fontaine、Ariën S Rustenburg、Salah Salah、M R Gunner、John D Chodera、Justin R Cross、Craig B Thompson

  DOI：10.1038/nchembio.2307

  日期：2017.5

  Acidification enhances lactate dehydrogenase– and malate dehydrogenase–mediated promiscuous production of L-2-hydroxyglutarate (L-2HG) from α-ketoglutarate and stabilizes HIF-1α levels. The metabolite 2-hydroxyglutarate (2HG) can be produced as either a D- R- or L- S- enantiomer, each of which inhibits α-ketoglutarate (αKG)-dependent enzymes involved in diverse biologic processes. Oncogenic mutations in isocitrate dehydrogenase (IDH) produce D-2HG, which causes a pathologic blockade in cell differentiation. On the other hand, oxygen limitation leads to accumulation of L-2HG, which can facilitate physiologic adaptation to hypoxic stress in both normal and malignant cells. Here we demonstrate that purified lactate dehydrogenase (LDH) and malate dehydrogenase (MDH) catalyze stereospecific production of L-2HG via 'promiscuous' reduction of the alternative substrate αKG. Acidic pH enhances production of L-2HG by promoting a protonated form of αKG that binds to a key residue in the substrate-binding pocket of LDHA. Acid-enhanced production of L-2HG leads to stabilization of hypoxia-inducible factor 1 alpha (HIF-1α) in normoxia. These findings offer insights into mechanisms whereby microenvironmental factors influence production of metabolites that alter cell fate and function.

  酸化作用增强乳酸脱氢酶和苹果酸脱氢酶介导的从α-酮戊二酸产生L-2-羟基戊二酸（L-2HG）的非特异性反应，并稳定HIF-1α水平。代谢物2-羟基戊二酸（2HG）可以作为D-R-或L-S-手性异构体产生，每种都能抑制涉及多种生物过程的α-酮戊二酸（αKG）依赖性酶。异柠檬酸脱氢酶（IDH）的致癌突变产生D-2HG，导致细胞分化的病理阻断。另一方面，氧气限制导致L-2HG积累，这可以促进正常细胞和恶性细胞对低氧应激的生理适应。在此，我们证明纯化的乳酸脱氢酶（LDH）和苹果酸脱氢酶（MDH）通过非特异性还原替代底物αKG，催化特异性产生L-2HG。酸性pH通过促进αKG的质子化形式，该形式结合到LDHA的底物结合口袋中的关键残基，从而增强L-2HG的产生。酸增强的L-2HG产生导致在常氧条件下稳定缺氧诱导因子1α（HIF-1α）。这些发现提供了关于微环境因素如何影响代谢物产生，从而改变细胞命运和功能的机制的见解。
• 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%。
• Kinetic Mechanism and Structural Requirements of the Amine-Catalyzed Decarboxylation of Oxaloacetic Acid
  作者：Nabil K. Thalji、William E. Crowe、Grover L. Waldrop

  DOI：10.1021/jo8014648

  日期：2009.1.2

  and chemical mechanism of amine-catalyzed decarboxylation of oxaloacetic acid at pH 8.0 has been reevaluated using a new and versatile assay. Amine-catalyzed decarboxylation of oxaloacetic acid proceeds via the formation of an imine intermediate, followed by decarboxylation of the intermediate and hydrolysis to yield pyruvate. The decrease in oxaloacetic acid was coupled to NADH formation by malate dehydrogenase

  使用新的通用分析方法，已重新评估了pH 8.0时胺催化草酰乙酸脱羧的动力学和化学机理。通过形成亚胺中间体进行胺催化的草酰乙酸脱羧，然后使该中间体脱羧并水解以产生丙酮酸盐。草酸乙酸的减少与苹果酸脱氢酶与NADH的形成有关，这可以确定最初的甲醇胺形成（作为酰亚胺化步骤的一部分）和脱羧的速率。通过比较观察到的各种胺，特别是二胺的速率，确定了在pH 8.0下二胺催化脱羧的结构和电子要求。在pH 8.0下，发现单胺是非常差的催化剂，而有些二胺 最值得注意的是乙二胺，是出色的催化剂。结果表明，二胺的第二个氨基基团通过在甲醇胺形成步骤中充当质子穿梭，提高了亚胺的形成速率，这使二胺能够克服高水平的溶剂化作用，否则溶剂化会抑制甲醇胺的形成，从而抑制亚胺的形成。第二氨基的存在还可以提高甲醇胺脱水步骤的速率。与以前的报告相反，第二个氨基通过氢键结合到亚胺氮上来提高脱羧速率，从而稳定了在脱羧过程中在亚胺上产生的负
• Mechanistic Studies on Tryptophan Lyase (NosL): Identification of Cyanide as a Reaction Product
  作者：Dhananjay M. Bhandari、Dmytro Fedoseyenko、Tadhg P. Begley

  DOI：10.1021/jacs.7b09000

  日期：2018.1.17

  Tryptophan lyase (NosL) catalyzes the formation of 3-methylindole-2-carboxylic acid and 3-methylindole from l-tryptophan. In this paper, we provide evidence supporting a formate radical intermediate and demonstrate that cyanide is a byproduct of the NosL-catalyzed reaction with l-tryptophan. These experiments require a major revision of the NosL mechanism and uncover an unanticipated connection between

  色氨酸裂解酶 (NosL) 催化 3-甲基吲哚-2-羧酸和 3-甲基吲哚从 l-色氨酸形成。在本文中，我们提供了支持甲酸自由基中间体的证据，并证明氰化物是 NosL 催化与 l-色氨酸反应的副产物。这些实验需要对 NosL 机制进行重大修改，并揭示 NosL 和 HydG 之间的意外联系，HydG 是一种自由基 SAM 酶，在 [Fe-Fe] 氢化酶的金属簇生物合成过程中，由酪氨酸形成氰化物和一氧化碳。