2,3-Dihydroxy-5-oxo-hexanedioate

• 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
• 英文名称: 2,3-Dihydroxy-5-oxo-hexanedioate
• 英文别名: (2R,3S)-2,3-dihydroxy-5-oxohexanedioate
• 化学式: C6H6O7-2
• 分子量: 190.11
• InChiKey: QUURPCHWPQNNGL-ZAFYKAAXSA-L

计算性质

• 辛醇/水分配系数(LogP)：
  -0.8
• 重原子数：
  13
• 可旋转键数：
  3
• 环数：
  0.0
• sp3杂化的碳原子比例：
  0.5
• 拓扑面积：
  138
• 氢给体数：
  2
• 氢受体数：
  7

反应信息

• 作为反应物：
  描述：

  2,3-Dihydroxy-5-oxo-hexanedioate 生成 2-Hydroxy-3-oxopropanoate 、 piruvate
  参考文献：
  名称：

  Rhombohedral crystals of 2-dehydro-3-deoxygalactarate aldolase from Escherichia coli

  摘要：

  2-去氢-3-脱氧半乳糖酸醛酸（DDG）醛酸裂解酶（E.C. 4.1.2.20）催化DDG和2-去氢-3-脱氧葡萄糖酸的可逆醛基断裂生成丙酮酸和酒石酸半醛。从大肠杆菌K-12的重组DDG醛酸裂解酶中获得了菱形晶体。晶体属于空间群R32，具有晶胞参数a=93 Å，α=85°。晶体在Cu Kα旋转阳极发生器上的分辨率超过1.8 Å。不对称单元可能包含两个分子，对应于1.34 Å3 Da-1的填充密度。

  DOI：

  10.1107/s0907444999006502
• 作为产物：
  描述：

  D-saccharate 生成 2,3-Dihydroxy-5-oxo-hexanedioate 、 水
  参考文献：
  名称：

  New Insights into the Alternative d-Glucarate Degradation Pathway

  摘要：

  Although the D-glucarate degradation pathway is well characterized in Escherichia coli, genetic and biochemical information concerning the alternative pathway proposed in Pseudomonas species and Bacillus subtilis remains incomplete. Acinetobacter baylyi ADP1 is a Gram-negative soil bacterium possessing the alternative pathway and able to grow using D-glucarate as the only carbon source. Based on the annotation of its sequenced genome (1), we have constructed a complete collection of single-gene deletion mutants (2). High throughput profiling for growth on a minimal medium containing D-glucarate as the only carbon source for similar to 2450 mutants led to the identification of the genes involved in D-glucarate degradation. Protein purification after recombinant production in E. coli allowed us to reconstitute the enzymatic pathway in vitro. We describe here the kinetic characterization of D-glucarate dehydratase, D-5-keto-4-deoxyglucarate dehydratase, and of cooperative alpha-ketoglutarate semialdehyde dehydrogenase. Transcription and expression analyses of the genes involved in D-glucarate metabolism within a single organism made it possible to access information regarding the regulation of this pathway for the first time.

  DOI：

  10.1074/jbc.m800487200

文献信息

• Evolution of Enzymatic Activities in the Enolase Superfamily:  <scp>l</scp>-Talarate/Galactarate Dehydratase from <i>Salmonella typhimurium</i> LT2^,
  作者：Wen Shan Yew、Alexander A. Fedorov、Elena V. Fedorov、Steven C. Almo、John A. Gerlt

  DOI：10.1021/bi7008882

  日期：2007.8.1

  competition with dehydration, we conclude that Lys 197 functions as the galactarate-specific base and His 328 functions as the l-talarate-specific base. The epimerization of l-talarate to galactarate that competes with dehydration can be rationalized by partitioning of the enolate intermediate between dehydration (departure of the 3-OH group catalyzed by the conjugate acid of His 328) and epimerization (protonation

  我们将l-talarate脱水酶（TalrD）和galactarate脱水酶（GalrD）功能分配给了机制多样的烯醇化酶超家族中的一组直系同源蛋白，重点研究了鼠伤寒沙门氏菌LT2基因组（GI：16766982; STM3697）编码的蛋白。像同源扁桃酸酯消旋酶，l-富康酸酯脱水酶和d-酒石酸脱水酶一样，TalrD / GalrD的活性位点在（beta / alpha）7beta-桶结构域，Asp 226，Glu 252和Glu 278作为第三，第四和第五个β链末端的必需Mg2 +的配体，第七个末端的通用酸/碱His 328-Asp 301二聚体和第六个β链，以及在第八个β链末端的亲电子Glu 348。我们通过筛选糖库发现了STM3697的功能。它催化l-酒石酸盐（kcat = 2.1 s-1，kcat / Km = 9.1 x 10（3）M-1 s-1）和半乳糖酸盐（kcat = 3.5 s-1，kcat
• Computation-Facilitated Assignment of the Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase from <i>Oceanobacillus iheyensis</i>,
  作者：John F. Rakus、Chakrapani Kalyanaraman、Alexander A. Fedorov、Elena V. Fedorov、Fiona P. Mills-Groninger、Rafael Toro、Jeffrey Bonanno、Kevin Bain、J. Michael Sauder、Stephen K. Burley、Steven C. Almo、Matthew P. Jacobson、John A. Gerlt

  DOI：10.1021/bi901731c

  日期：2009.12.8

  l-talarate/galactarate dehydratase (TalrD/GalrD). On the basis of the different active site structures and different regiochemistries, we recognize that these functions represent an example of apparent, not actual, convergent evolution of function. The structure of GalrD-II and its active site architecture allow identification of the seventh functionally and structurally characterized subgroup in the enolase superfamily

  来自Oceanobacillus iheyensis （GI 23100298，IMG 基因座标签 Ob2843，PDB 条目 2OQY）的烯醇化酶超家族的未表征成员的结构由纽约 SGX 结构基因组学研究中心 (NYSGXRC) 确定。该结构包含两个 Mg 2+离子，彼此相距 10.4 Å，其中一个位于 (β/α) 7中的规范位置β-桶结构域（尽管第五条 β-链末端的配体是 His，在超家族的结构特征成员中是前所未有的）；第二个位于加帽域内的一个新站点。将单糖和二糖库与活性位点进行计算机对接，预测二糖可能是底物。酸糖物理库的活性筛选将半乳糖二酸鉴定为底物 ( k cat = 6.8 s −1 , K M = 620 μM, k cat / K M = 1.1 × 10 4 M −1 s −1), 允许将 Ob2843 功能分配为半乳糖二酸脱水酶 (GalrD-II)。催化受损的 Y90F 突变体与
• Purification, crystallization and structural elucidation of<scp>D</scp>-galactaro-1,4-lactone cycloisomerase from<i>Agrobacterium tumefaciens</i>involved in pectin degradation
  作者：Matthew W. Vetting、Jason T. Bouvier、John A. Gerlt、Steven C. Almo

  DOI：10.1107/s2053230x15023286

  日期：2016.1.1

  six‐carbon acid sugar that is degraded in a five‐step pathway to central metabolic intermediates by some bacteria, including Agrobacterium tumefaciens. In the third step of the pathway, D‐galactaro‐1,4‐lactone is converted to 2‐keto‐3‐deoxy‐L‐threo‐hexarate by a member of the mandelate racemase subgroup of the enolase superfamily with a novel activity for the superfamily. The 1.6 Å resolution structure

  果胶存在于植物细胞壁中，通常被作为废物丢弃。许多研究小组有兴趣将这种生物质废物流重新用于燃料和大宗化学品的生产。这种多糖的主要单体亚基是 D-半乳糖醛酸，这是一种六碳酸糖，可通过一些细菌（包括根癌农杆菌）通过五步途径降解为中心代谢中间体。在该途径的第三步中，D-半乳糖苷-1,4-内酯被烯醇酶超家族的扁桃酸消旋酶亚组的成员转化为 2-酮-3-脱氧-L-苏式-六酸酯，具有以下新活性：超家族。确定了该酶的 1.6 Å 分辨率结构，揭示了整体修饰的 (β/α) 7 β TIM 桶结构域，这是该超家族的标志。D-Galactaro-1,4-内酯手动对接至位于 N 端盖结构域和 C 端桶结构域之间界面的活性位点。根据内酯在活性位点中的位置，Lys166 预计是负责提取 α 质子的活性位点碱基。预计活性位点另一侧的 His296 是在内酯环打开时向 β 碳提供质子的一般酸。内酯环似乎通过与 Trp298
• Galactaro δ-Lactone Isomerase: Lactone Isomerization by a Member of the Amidohydrolase Superfamily
  作者：Jason T. Bouvier、Fiona P. Groninger-Poe、Matthew Vetting、Steven C. Almo、John A. Gerlt

  DOI：10.1021/bi5000492

  日期：2014.2.4

  Agrobacterium tumefaciens strain C58 can utilize D-galacturonate as a sole source of carbon via a pathway in which the first step is oxidation of D-galacturonate to D-galactaro-1,5-lactone. We have identified a novel enzyme, D-galactarolactone isomerase (GLI), that catalyzes the isomerizaton of D-galactaro-1,5-lactone to D-galactaro-1,4-lactone. GLI; a member of the functionally diverse amidohydrolase superfamily, is a homologue of LigI that catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate in lignin degradation. The ability of GLI to catalyze lactone isomerization instead of hydrolysis can be explained by the absence of the general basic catalysis used by 2-pyrone-4,6-dicarbolcylate lactonase.
• Evolution of Enzymatic Activities in the Enolase Superfamily:  Characterization of the (<i>D</i>)-Glucarate/Galactarate Catabolic Pathway in <i>Escherichia coli</i>
  作者：Brian K. Hubbard、Marjan Koch、David R. J. Palmer、Patricia C. Babbitt、John A. Gerlt

  DOI：10.1021/bi981124f

  日期：1998.10.1

  The genes encoding the enzymes in the (D)-glucarate/galactarate catabolic pathway have been identified in the Escherichia coli genome. These encode, in three transcriptional units, (D)-glucarate dehydratase (GlucD), galactarate dehydratase, 5-keto-4-deoxy-(D)-glucarate aldolase, tartronate semialdehyde reductase, a glycerate kinase that generates 2-phosphoglycerate as product, and two hexaric acid transporters. We also have identified a gene proximal to that encoding GlucD that encodes a protein that is 72% identical in primary sequence to GlucD (GlucD-related protein or GlucDRP). However, whereas GlucD catalyzes the efficient dehydration of both (D)-glucarate and (L)-idarate as well as their epimerization, GlucDRP is significantly impaired in both reactions. Perhaps GlucDRP is an example of gene duplication and evolution in progress in the E. coli chromosome.