D-isocitrate

• 分子结构分类: 有机化合物 - 有机酸及其衍生物 - 羧酸及其衍生物
• 英文名称: D-isocitrate
• 英文别名: threo-Ds-isocitrate；(1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate
• 化学式: C₆H₅O₇
• 分子量: 189.101
• InChiKey: ODBLHEXUDAPZAU-ZAFYKAAXSA-K

计算性质

• 辛醇/水分配系数(LogP)：
  0.1
• 重原子数：
  13
• 可旋转键数：
  2
• 环数：
  0.0
• sp3杂化的碳原子比例：
  0.5
• 拓扑面积：
  141
• 氢给体数：
  1
• 氢受体数：
  7

反应信息

• 作为反应物：
  描述：

  D-isocitrate 生成 isocitrate
  参考文献：
  名称：

  摘要：

  DOI：
• 作为产物：
  描述：

  2-羟基丙烷-1,2,3-三羧酸根 生成 D-isocitrate
  参考文献：
  名称：

  乌头酸酶的晶体结构具有反式阿卡奈酸酯和亚硝酸柠檬酸酯的结合。

  摘要：

  线粒体乌头酸酶的晶体结构与抑制剂反式-花生酸酯和硝酸柠檬酸酯键合到[4Fe-4S]簇上，已得到解析并以2.05 A的分辨率进行精制，R因子分别为0.168和0.172。乌头酸酶与柠檬酸和顺式衣康酸的底物结晶是不可能的，因为该酶会翻转并选择结合了异柠檬酸的酶进入晶格。因此，我们分析了与这两种底物的抑制剂类似物复合的酶的晶体结构。结合硝酸柠檬酸盐的结构提供了柠檬酸盐结合的模型。具有反式-aconitate键的结构以两种方式提供了顺式-aconitate键合的模型：[4Fe-4S]簇的Fe4为五坐标，并且C beta位置的碳为三角形。这些结果使得反应机理的模型可以扩展到乌头酸酶的所有三种天然底物。结果支持了一个模型，其中柠檬酸盐和异柠檬酸盐形成相似的螯合物结构，绕Cα-Cβ键旋转180度，而中间的顺式-酸酯以两种方式（柠檬酸盐模式或异柠檬酸盐模式）结合。在两种抑制剂配合物中，H2O分子也与Fe4

  DOI：

  10.1006/jmbi.1994.1246

文献信息

• Evaluation by Mutagenesis of the Importance of 3 Arginines in α, β, and γ Subunits of Human NAD-dependent Isocitrate Dehydrogenase
  作者：Sambanthamurthy Soundar、Jung-Hoon Park、Tae-Lin Huh、Roberta F. Colman

  DOI：10.1074/jbc.m306178200

  日期：2003.12

  NAD-dependent isocitrate dehydrogenase is an allosteric enzyme, activated by ADP and composed of 3 distinct subunits in the ratio 2alpha:1beta:1gamma. Based on the crystal structure of NADP-dependent isocitrate dehydrogenases from Escherichia coli, Bacillus subtilis, and pig heart, and a comparison of their amino acid sequences, alpha-Arg88, beta-Arg99, and gamma-Arg97 of human NAD-dependent isocitrate dehydrogenase

  哺乳动物NAD依赖性异柠檬酸脱氢酶是一种变构酶，由ADP激活，由3个不同的亚基组成，比例为2alpha：1beta：1gamma。基于大肠杆菌，枯草芽孢杆菌和猪心脏的NADP依赖性异柠檬酸脱氢酶的晶体结构，以及人NAD依赖性异柠檬酸脱氢酶的氨基酸序列，α-Arg88，β-Arg99和γ-Arg97的比较选择它们作为诱变的候选物，以测试它们在催化活性和ADP活化中的作用。带有cDNA的质粒，该cDNA编码人异柠檬酸脱氢酶（Kim，YO，Koh，HJ，Kim，SH，Jo，SH，Huh，JW，Jeong，KS，Lee，IJ，Song，BJ和Huh，TL（1999）J. Biol。Chem。274，36866-36875）用于在异柠檬酸脱氢酶缺陷型大肠杆菌中表达该酶。将野生型（WT）和突变酶（每个酶包含2个正常亚基以及一个具有alpha-R88Q，beta-R99Q或gamma-R97Q的突变亚基
• Bifunctional isocitrate–homoisocitrate dehydrogenase: A missing link in the evolution of β-decarboxylating dehydrogenase
  作者：Kentaro Miyazaki

  DOI：10.1016/j.bbrc.2005.03.169

  日期：2005.5

  not require leucine, glutamate, or lysine for growth; the single pathway might play multiple (i.e., ancestral) roles in amino acid biosynthesis. The PH1722 gene was cloned and expressed in Escherichia coli and the substrate specificity of the recombinant enzyme was investigated. It exhibited activities on isocitrate and homoisocitrate at near equal efficiency, but not on 3-isopropylmalate. PH1722 is

  β-脱羧脱氢酶包括3-异丙基苹果酸脱氢酶，异柠檬酸脱氢酶和均异柠檬酸脱氢酶。它们具有高度的氨基酸序列同一性，并分别在亮氨酸，谷氨酸和赖氨酸的氨基酸生物合成途径中占据等效位置。因此，不仅酶，而且整个途径都应该从共同的祖先途径进化而来。在果球菌中，在基因组序列中只鉴定了三个途径中的一个，而PH1722是唯一的β-脱羧脱氢酶基因。该生物不需要亮氨酸，谷氨酸或赖氨酸即可生长；单一途径可能在氨基酸生物合成中发挥多种（即祖先）作用。克隆并在大肠杆菌中表达了PH1722基因，并研究了重组酶的底物特异性。它对异柠檬酸和均异柠檬酸的活性几乎相同，但对3-异丙基苹果酸没有活性。因此，PH1722是一种新型的双功能β-脱羧脱氢酶，它可能在体内谷氨酸和赖氨酸的生物合成中起双重作用。
• AcnC of Escherichia coli is a 2-methylcitrate dehydratase (PrpD) that can use citrate and isocitrate as substrates
  作者：Lindsay Blank、Jeffrey Green、John R Guest

  DOI：10.1099/00221287-148-1-133

  日期：2002.1.1

  Escherichia coli possesses two well-characterized aconitases (AcnA and AcnB) and a minor activity (designated AcnC) that is retained by acnAB double mutants and represents no more than 5% of total wild-type aconitase activity. Here it is shown that a 2-methylcitrate dehydratase (PrpD) encoded by the prpD gene of the propionate catabolic operon (prpRBCDE) is identical to AcnC. Inactivation of prpD abolished the residual aconitase activity of an AcnAB-null strain, whereas inactivation of ybhJ, an unidentified acnA paralogue, had no significant effect on AcnC activity. Purified PrpD catalysed the dehydration of citrate and isocitrate but was most active with 2-methylcitrate. PrpD also catalysed the dehydration of several other hydroxy acids but failed to hydrate cis-aconitate and related substrates containing double bonds, indicating that PrpD is not a typical aconitase but a dehydratase. Purified PrpD was shown to be a monomeric iron–sulphur protein (M r 54000) having one unstable [2Fe–2S] cluster per monomer, which is needed for maximum catalytic activity and can be reconstituted by treatment with Fe2+ under reducing conditions.

  大肠杆菌有两种特征明显的乙酰辅酶A脱氢酶（AcnA和AcnB），还有一种活性较弱（称为AcnC）的乙酰辅酶A脱氢酶，由acnAB双突变体保留，占野生型乙酰辅酶A脱氢酶总活性的5%以下。研究表明，丙酸盐分解代谢基因簇（prpRBCDE）中的prpD基因编码的2-甲基柠檬酸脱氢酶（PrpD）与AcnC相同。prpD失活后，AcnAB-null菌株的剩余乙酰辅酶A脱氢酶活性消失，而未鉴定的乙酰辅酶A脱氢酶同源物ybhJ失活后，对AcnC活性没有显著影响。纯化的PrpD催化柠檬酸和异柠檬酸脱水，但对2-甲基柠檬酸的活性最高。PrpD还催化其他几种羟基酸的脱水，但不能水合顺式乙酰辅酶A和含有双键的相关底物，这表明PrpD不是典型的乙酰辅酶A脱氢酶，而是脱水酶。纯化的PrpD是一种单体铁硫蛋白（M r 54000），每个单体有一个不稳定的[2Fe-2S]簇，这是最大催化活性所需的，在还原条件下用Fe2+处理可以重建。
• Characterization of the isocitrate lyase gene from Corynebacterium glutamicum and biochemical analysis of the enzyme
  作者：D J Reinscheid、B J Eikmanns、H Sahm

  DOI：10.1128/jb.176.12.3474-3483.1994

  日期：1994.6

  Isocitrate lyase is a key enzyme in the glyoxylate cycle and is essential as an anaplerotic enzyme for growth on acetate as a carbon source. It is assumed to be of major importance in carbon flux control in the amino acid-producing organism Corynebacterium glutamicum. In crude extracts of C. glutamicum, the specific activities of isocitrate lyase were found to be 0.01 U/mg of protein after growth on glucose and 2.8 U/mg of protein after growth on acetate, indicating tight regulation. The isocitrate lyase gene, aceA, was isolated, subcloned, and characterized. The predicted gene product of aceA consists of 432 amino acids (M(r), 47,228) and shows up to 57% identity to the respective enzymes from other organisms. Downstream of aceA, a gene essential for thiamine biosynthesis was identified. Overexpression of aceA in C. glutamicum resulted in specific activities of 0.1 and 7.4 U/mg of protein in minimal medium containing glucose and acetate, respectively. Inactivation of the chromosomal aceA gene led to an inability to grow on acetate and to the absence of any detectable isocitrate lyase activity. Isocitrate lyase was purified to apparent homogeneity and subjected to biochemical analysis. The native enzyme was shown to be a tetramer of identical subunits, to exhibit an ordered Uni-Bi mechanism of catalysis, and to be effectively inhibited by 3-phosphoglycerate, 6-phosphogluconate, phosphoenolpyruvate, fructose-1,6-bisphosphate, and succinate.

  异柠檬酸裂解酶是甘氧酸循环中的关键酶，对于以乙酸为碳源生长的生长必须作为一种补充酶。在氨基酸生产菌科林杆菌属谷氨酸杆菌中，它被认为在碳通量控制中具有重要作用。在C. glutamicum的粗提取物中，异柠檬酸裂解酶的比活性在葡萄糖生长后为0.01 U/mg蛋白质，在乙酸生长后为2.8 U/mg蛋白质，表明受到严格调控。异柠檬酸裂解酶基因aceA被分离、亚克隆并且进行了表征。aceA的预测基因产物由432个氨基酸（M(r)，47,228）组成，与其他生物中的相应酶具有高达57％的同源性。在aceA的下游，鉴定了一种合成硫胺素必需的基因。在C. glutamicum中过表达aceA导致最小培养基中的特定活性分别为0.1和7.4 U/mg蛋白质。在染色体上敲除aceA基因导致无法在乙酸上生长并且无法检测到任何异柠檬酸裂解酶活性。异柠檬酸裂解酶被纯化到表观同质性并进行了生化分析。原生酶被证明是相同亚基的四聚体，表现出有序的Uni-Bi催化机制，并且被3-磷酸甘油酸、6-磷酸葡萄糖酸、磷酸烯醇丙酮酸、果糖-1,6-二磷酸和琥珀酸有效地抑制。
• Characterization of Activity and Expression of Isocitrate Lyase in <i>Mycobacterium avium</i> and <i>Mycobacterium tuberculosis</i>
  作者：Kerstin Höner Zu Bentrup、Andras Miczak、Dana L. Swenson、David G. Russell

  DOI：10.1128/jb.181.23.7161-7167.1999

  日期：1999.12

  Analysis by two-dimensional gel electrophoresis revealed that Mycobacterium avium expresses several proteins unique to an intracellular infection. One abundant protein with an apparent molecular mass of 50 kDa was isolated, and the N-terminal sequence was determined. It matches a sequence in the M. tuberculosis database (Sanger) with similarity to the enzyme isocitrate lyase of both Corynebacterium glutamicum and Rhodococcus fascians . Only marginal similarity was observed between this open reading frame (ORF) (termed icl ) and a second distinct ORF (named aceA ) which exhibits a low similarity to other isocitrate lyases. Both ORFs can be found as distinct genes in the various mycobacterial databases recently published. Isocitrate lyase is a key enzyme in the glyoxylate cycle and is essential as an anapleurotic enzyme for growth on acetate and certain fatty acids as carbon source. In this study we express and purify Icl, as well as AceA proteins, and show that both exhibit isocitrate lyase activity. Various known inhibitors for isocitrate lyase were effective. Furthermore, we present evidence that in both M. avium and M. tuberculosis the production and activity of the isocitrate lyase is enhanced under minimal growth conditions when supplemented with acetate or palmitate.

  摘要 二维凝胶电泳分析表明 分枝杆菌 表达几种细胞内感染特有的蛋白质。分离出一种表观分子量为 50 kDa 的丰富蛋白质，并确定了其 N 端序列。它与 结核杆菌 数据库（桑格）中的序列相吻合，与谷氨酸棒状杆菌（Corynebacterium）的异柠檬酸酶（isocitrate lyase）相似。 谷氨酸棒杆菌 和 法氏红球菌 .该开放阅读框（ORF）（称为 icl ）和第二个不同的 ORF（名为 aceA )之间的相似性很低。在最近公布的各种分枝杆菌数据库中，这两个 ORF 都是不同的基因。异柠檬酸裂解酶是乙醛酸循环中的一种关键酶，也是以乙酸和某些脂肪酸为碳源的生长所必需的一种无酵素酶。在这项研究中，我们表达并纯化了 Icl 和 AceA 蛋白，结果表明两者都具有异柠檬酸裂解酶活性。各种已知的异柠檬酸裂解酶抑制剂均有效。此外，我们还提出证据表明，在 禽霉菌 和 结核杆菌 在最低生长条件下，当补充乙酸盐或棕榈酸盐时，异柠檬酸酯裂解酶的产生和活性都会增强。