shikimate

• 分子结构分类: 有机化合物 - 有机氧化合物
• 英文名称: shikimate
• 英文别名: (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate；(3R,4S,5R)-3,4,5-trihydroxycyclohexene-1-carboxylate
• 化学式: C₇H₉O₅
• 分子量: 173.145
• InChiKey: JXOHGGNKMLTUBP-HSUXUTPPSA-M

计算性质

• 辛醇/水分配系数(LogP)：
  -1.1
• 重原子数：
  12
• 可旋转键数：
  0
• 环数：
  1.0
• sp3杂化的碳原子比例：
  0.57
• 拓扑面积：
  101
• 氢给体数：
  3
• 氢受体数：
  5

反应信息

• 作为反应物：
  描述：

  a quinone 、 shikimate 生成 3-dehydroshikimate 、 a quinol
  参考文献：
  名称：

  3-Dehydroquinate Production by Oxidative Fermentation and Further Conversion of 3-Dehydroquinate to the Intermediates in the Shikimate Pathway

  摘要：

  研究人员首次分析了醋酸细菌中的葡萄糖菌株通过氧化发酵从醌酸产生3-脱氢醌酸的过程。在细菌膜中，醌脱氢酶是一种典型的醌蛋白，含有吡咯喹啉醌（PQQ）作为辅酶，是醌氧化的主要酶。在早期生长阶段，奎宁酸被氧化成 3-脱氢奎宁酸，最终产量几乎达到 100%。研究发现，葡萄糖杆菌菌株的静止细胞、干燥细胞、固定化细胞或固定化膜部分是奎宁酸氧化的有效生物催化剂。生长细胞和固定化细胞可将 3-脱氢醌进一步转化为 3-脱氢ikimate，且产量合理。在同一生物体的可溶性馏分中检测到了3-脱氢醌脱水酶和依赖于NADP的莽草酸脱氢酶的强酶活性，并且它们之间有部分分离。由于莽草酸途径在新陈代谢途径中远离葡萄糖，因此从醌到3-脱氢醌进入莽草酸途径看起来有利于产生莽草酸途径的新陈代谢中间产物。

  DOI：

  10.1271/bbb.67.2124
• 作为产物：
  描述：

  3-dehydroshikimate 在 乙二胺四乙酸 、 葡萄糖 、 nicotinamide adenine dinucleotide phosphate 、 glucose dehydrogenase immobilised on BD-Sepharose 4B 、 shikimate dehydrogenase immobilised on BD-Sepharose 4B 、 2-巯基乙醇 作用下， 生成 shikimate
  参考文献：
  名称：

  Conversion of Quinate to 3-Dehydroshikimate by Ca-Alginate-Immobilized Membrane ofGluconobacter oxydansIFO 3244 and Subsequent Asymmetric Reduction of 3-Dehydroshikimate to Shikimate by Immobilized Cytoplasmic NADP-Shikimate Dehydrogenase

  摘要：

  将 Gluconobacter oxydans IFO 3244 的膜部分固定到 Ca-alginate 珠中，其中涉及膜结合的醌蛋白醌脱氢酶和 3-脱氢醌脱水酶。在中性 pH 条件下，固定了 Ca-alginate 的细菌膜催化了奎宁酸氧化为 3-脱氢奎宁酸并自发转化为 3-脱氢ikimate的连续反应。从醌酯到 3-脱氢ikimate的转化率几乎达到 100%。来自同一生物体的依赖于 NADP 的细胞质酶、莽草酸脱氢酶和 d-葡萄糖脱氢酶与不同的载体固定在一起，作为从 3-脱氢莽草酸生成莽草酸的不对称还原系统。蓝色葡聚糖 2000、蓝色葡聚糖-Sepharose-4B、DEAE-Sephadex A-50、DEAE-纤维素和羟基磷灰石是这两种细胞质酶的有效载体，最初加入的 3-脱氢莽草酸以 100% 的产率转化为莽草酸。两种细胞质酶对蓝色葡聚糖 2000 表现出很强的亲和力，并形成了一种可溶性固定化催化剂，其催化效率与游离酶相同。本文可能是第一篇成功固定化 NAD（P）依赖性脱氢酶的论文。

  DOI：

  10.1271/bbb.100497

文献信息

• Archaeal Shikimate Kinase, a New Member of the GHMP-Kinase Family
  作者：Matthew Daugherty、Veronika Vonstein、Ross Overbeek、Andrei Osterman

  DOI：10.1128/jb.183.1.292-300.2001

  日期：2001.1

  Shikimate kinase (EC2.7.1.71) is a committed enzyme in the seven-step biosynthesis of chorismate, a major precursor of aromatic amino acids and many other aromatic compounds. Genes for all enzymes of the chorismate pathway except shikimate kinase are found in archaeal genomes by sequence homology to their bacterial counterparts. In this study, a conserved archaeal gene (gi‖1500322 inMethanococcus jannaschii) was identified as the best candidate for the missing shikimate kinase gene by the analysis of chromosomal clustering of chorismate biosynthetic genes. The encoded hypothetical protein, with no sequence similarity to bacterial and eukaryotic shikimate kinases, is distantly related to homoserine kinases (EC2.7.1.39) of the GHMP-kinase superfamily. The latter functionality inM. jannaschiiis assigned to another gene (gi‖1591748), in agreement with sequence similarity and chromosomal clustering analysis. Both archaeal proteins, overexpressed inEscherichia coliand purified to homogeneity, displayed activity of the predicted type, with steady-state kinetic parameters similar to those of the corresponding bacterial kinases:K_m,shikimate= 414 ± 33 μM,K_m,ATP= 48 ± 4 μM, andk_cat= 57 ± 2 s⁻¹for the predicted shikimate kinase andK_m,homoserine= 188 ± 37 μM,K_m,ATP= 101 ± 7 μM, andk_cat= 28 ± 1 s⁻¹for the homoserine kinase. No overlapping activity could be detected between shikimate kinase and homoserine kinase, both revealing a >1,000-fold preference for their own specific substrates. The case of archaeal shikimate kinase illustrates the efficacy of techniques based on reconstruction of metabolism from genomic data and analysis of gene clustering on chromosomes in finding missing genes.

  摘要莽草酸激酶（EC2.7.1.71）是雏菊酸七步生物合成过程中的一个重要酶，雏菊酸是芳香族氨基酸和许多其他芳香族化合物的主要前体。除了莽草酸激酶之外，所有雏菊酯途径酶的基因都可以通过与细菌同源基因的序列同源性在古细菌基因组中找到。在本研究中，通过对雏菊酸盐生物合成基因的染色体聚类分析，确定了一个保守的古细菌基因（Methanococcus jannaschii 的 gi‖1500322）为缺失的雏菊酸盐激酶基因的最佳候选者。所编码的假定性蛋白与细菌和真核生物的莽草酸激酶没有序列相似性，但与 GHMP 激酶超家族的高丝氨酸激酶（EC2.7.1.39）关系密切。与序列相似性和染色体聚类分析一致，后者在 M. jannaschii 中被归入另一个基因（gi‖1591748）。这两种古生物蛋白在大肠杆菌中过度表达并纯化后，都显示出预测类型的活性，其稳态动力学参数与相应的细菌激酶相似：预测的莽草酸激酶的 Km，shikimate= 414 ± 33 μM，Km，ATP= 48 ± 4 μM，kcat= 57 ± 2 s-1；高丝氨酸激酶的 Km，homoserine= 188 ± 37 μM，Km，ATP= 101 ± 7 μM，kcat= 28 ± 1 s-1。在莽草酸激酶和高丝氨酸激酶之间检测不到重叠的活性，两者都显示出对各自特定底物的1000倍偏好。古细菌莽草酸激酶的例子说明了基于基因组数据重建代谢和染色体上基因聚类分析的技术在寻找缺失基因方面的功效。
• The role of the C8 proton of ATP in the catalysis of shikimate kinase and adenylate kinase
  作者：Colin P Kenyon、Robyn L Roth

  DOI：10.1186/1471-2091-13-15

  日期：——

  It has been demonstrated that the adenyl moiety of ATP plays a direct role in the regulation of ATP binding and/or phosphoryl transfer within a range of kinase and synthetase enzymes. The role of the C8-H of ATP in the binding and/or phosphoryl transfer on the enzyme activity of a number of kinase and synthetase enzymes has been elucidated. The intrinsic catalysis rate mediated by each kinase enzyme is complex, yielding apparent KM values ranging from less than 0.4 μM to more than 1 mM for ATP in the various kinases. Using a combination of ATP deuterated at the C8 position (C8D-ATP) as a molecular probe with site directed mutagenesis (SDM) of conserved amino acid residues in shikimate kinase and adenylate kinase active sites, we have elucidated a mechanism by which the ATP C8-H is induced to be labile in the broader kinase family. We have demonstrated the direct role of the C8-H in the rate of ATP consumption, and the direct role played by conserved Thr residues interacting with the C8-H. The mechanism by which the vast range in KM might be achieved is also suggested by these findings. We have demonstrated the mechanism by which the enzyme activities of Group 2 kinases, shikimate kinase (SK) and adenylate kinase 1 (AK1), are controlled by the C8-H of ATP. Mutations of the conserved threonine residues associated with the labile C8-H cause the enzymes to lose their saturation kinetics over the concentration range tested. The relationship between the role C8-H of ATP in the reaction mechanism and the ATP concentration as they influence the saturation kinetics of the enzyme activity is also shown. The SDM clearly identified the amino acid residues involved in both the catalysis and regulation of phosphoryl transfer in SK and AK1 as mediated by C8H-ATP. The data outlined serves to demonstrate the “push” mechanism associated with the control of the saturation kinetics of Group 2 kinases mediated by ATP C8-H. It is therefore conceivable that kinase enzymes achieve the observed 2,500-fold variation in KM through a combination of the various conserved “push” and “pull” mechanisms associated with the release of C8-H, the proton transfer cascades unique to the class of kinase in question and the resultant/concomitant creation of a pentavalent species from the γ-phosphate group of ATP. Also demonstrated is the interplay between the role of the C8-H of ATP and the ATP concentration in the observed enzyme activity. The lability of the C8-H mediated by active site residues co-ordinated to the purine ring of ATP therefore plays a significant role in explaining the broad KM range associated with kinase steady state enzyme activities.

  研究表明，在一系列激酶和合成酶中，ATP 的腺嘌呤分子在调节 ATP 结合和/或磷酸转移方面发挥着直接作用。ATP 的 C8-H 在一些激酶和合成酶的酶活性的结合和/或磷酸转移中的作用已被阐明。每种激酶所介导的内在催化速率都很复杂，在各种激酶中，ATP 的表观 KM 值从小于 0.4 μM 到大于 1 mM 不等。利用在 C8 位氚化的 ATP（C8D-ATP）作为分子探针，并结合莽草酸激酶和腺苷酸激酶活性位点中保守氨基酸残基的定点突变（SDM），我们阐明了 ATP C8-H 在更广泛的激酶家族中诱导易变的机制。我们证明了 C8-H 在 ATP 消耗率中的直接作用，以及与 C8-H 相互作用的保守 Thr 残基所发挥的直接作用。这些发现还提出了可能实现巨大 KM 范围的机制。我们已经证明了第 2 组激酶、莽草酸激酶（SK）和腺苷酸激酶 1（AK1）的酶活性受 ATP 的 C8-H 控制的机制。与易变 C8-H 相关的保守苏氨酸残基发生突变，会导致酶在测试浓度范围内失去饱和动力学。还显示了 ATP 的 C8-H 在反应机制中的作用与 ATP 浓度之间的关系，因为它们会影响酶活性的饱和动力学。SDM 清楚地确定了 C8H-ATP 介导的 SK 和 AK1 中参与磷酸转移催化和调节的氨基酸残基。概述的数据证明了与 ATP C8-H 介导的第 2 组激酶饱和动力学控制相关的 "推动 "机制。因此可以想象，激酶是通过与 C8-H 释放有关的各种保守的 "推 "和 "拉 "机制、有关类激酶特有的质子转移级联以及由此/同时从 ATP 的γ-磷酸基产生的五价物种的组合，实现观察到的 2,500 倍的 KM 变化的。在观察到的酶活性中，ATP 的 C8-H 作用与 ATP 浓度之间的相互作用也得到了证明。因此，由与 ATP 的嘌呤环配合的活性位点残基介导的 C8-H 的不稳定性在解释与激酶稳态酶活性相关的宽 KM 范围方面起着重要作用。
• The 2.3-Å Crystal Structure of the Shikimate 5-Dehydrogenase Orthologue YdiB from Escherichia coli Suggests a Novel Catalytic Environment for an NAD-dependent Dehydrogenase
  作者：Jordi Benach、Insun Lee、William Edstrom、Alexandre P. Kuzin、Yiwen Chiang、Thomas B. Acton、Gaetano T. Montelione、John F. Hunt

  DOI：10.1074/jbc.m301348200

  日期：2003.5

  features, including a cysteine residue in close apposition to the nicotinamide ring and a clamp over the ribose of the adenosine moiety formed by phenylalanine and lysine residues. The structure explains the specificity for NAD versus NADP in different members of the shikimate dehydrogenase family on the basis of variations in the amino acid identity of several other residues in the vicinity of this ribose

  我们在这里介绍了大肠杆菌YdiB蛋白，,草酸5脱氢酶的直向同源物的2.3-A晶体结构。该酶催化3-脱氢shi草酸酯还原为sh草酸酯，这是the草酸酯途径的一部分，在哺乳动物中不存在，但在许多其他生物中是从头合成芳香族氨基酸，醌和叶酸所必需的。在这种情况下，the草酸酯途径已被推广为开发抗微生物剂的靶标。YdiB的晶体结构表明，protomer包含由两个alpha螺旋连接的两个alpha / beta结构域，其中N端结构域是新颖的，而C端结构域是Rossmann折叠。与该酶共纯化的NAD +辅因子与原R构象的烟酰胺环以延长的方式结合到Rossmann结构域。它的结合位点包含几个不同寻常的特征，包括与烟酰胺环紧靠的半胱氨酸残基和由苯丙氨酸和赖氨酸残基形成的腺苷部分的核糖上的钳位。该结构解释了基于该核糖基团附近其他几个残基的氨基酸同一性的变化，在the草酸脱氢酶家族的不同成员中NAD与NADP的
• Structure of <i>Arabidopsis</i> Dehydroquinate Dehydratase-Shikimate Dehydrogenase and Implications for Metabolic Channeling in the Shikimate Pathway^,
  作者：Sasha Anna Singh、Dinesh Christendat

  DOI：10.1021/bi060366+

  日期：2006.6.1

  The bifunctional enzyme dehydroquinate dehydratase-shikimate dehydrogenase (DHQ-SDH) catalyzes the dehydration of dehydroquinate to dehydroshikimate and the reduction of dehydroshikimate to shikimate in the shikimate pathway. We report the first crystal structure of Arabidopsis DHQ-SDH with shikimate bound at the SDH site and tartrate at the DHQ site. The interactions observed in the DHQ-tartrate complex

  双功能酶脱氢奎宁酸盐脱水酶-shi草酸酯脱氢酶（DHQ-SDH）催化sh草酸酯途径中的脱氢奎宁酸酯脱水为脱氢shi草酸酯和脱氢hydro草酸酯还原为sh草酸酯。我们报道了拟南芥DHQ-SDH的首个晶体结构，其sh草酸酯结合在SDH部位，酒石酸盐在DHQ部位。在酒石酸DHQ络合物中观察到的相互作用揭示了植物与微生物DHQ脱水酶家族中酶之间底物结合的保守模式。SDH-shi草酸酯络合物提供了活性位点残基在催化机制中的作用的第一个直接证据。定点诱变和机理分析表明，Asp 423和Lys 385是关键的催化基团，而Ser 336是关键的结合基团。
• Kinetic and chemical mechanisms of shikimate dehydrogenase from Mycobacterium tuberculosis
  作者：Isabel O. Fonseca、Rafael G. Silva、Claudia L. Fernandes、Osmar N. de Souza、Luiz A. Basso、Diógenes S. Santos

  DOI：10.1016/j.abb.2006.11.015

  日期：2007.1

  NADPH-dependent reduction of 3-dehydroshikimate. To gather information on the kinetic mechanism, initial velocity patterns, product inhibition, and primary deuterium kinetic isotope effect studies were performed and the results suggested a steady-state ordered bi-bi kinetic mechanism. The magnitudes of both primary and solvent kinetic isotope effects indicated that the hydride transferred from NADPH and

  结核分枝杆菌sh草酸脱氢酶（MtbSD）催化the草酸途径中的第四个反应，即NADPH依赖性的3-脱氢shi草酸还原。为了收集有关动力学机理的信息，进行了初始速度模式，产物抑制和主要的氘动力学同位素效应研究，结果表明稳态有序的双-bi动力学机理。伯和溶剂动力学同位素效应的大小都表明，在整个反应过程中，从NADPH转移的氢化物和从溶剂转移的质子在速率上没有明显的限制。质子库存分析表明，一个质子会引起溶剂同位素效应。多个同位素效应研究表明，氢化物和质子转移均是一致的。pH曲线表明，酸/碱化学反应发生在催化和底物结合中。通过同源建模在计算机上获得了MtbSD 3D模型。根据实验数据提出了MtbSD的动力学和化学机理。