D-erythrononate | 83313-10-4

• 分子结构分类: 有机化合物 - 有机氧化合物
• 英文名称: D-erythrononate
• 英文别名: D-erythronate；(2R,3R)-2,3,4-trihydroxybutanoate
• CAS: 83313-10-4
• 化学式: C₄H₇O₅
• 分子量: 135.097
• InChiKey: JPIJQSOTBSSVTP-PWNYCUMCSA-M

计算性质

• 辛醇/水分配系数(LogP)：
  -1.5
• 重原子数：
  9
• 可旋转键数：
  2
• 环数：
  0.0
• sp3杂化的碳原子比例：
  0.75
• 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：

  D-erythrononate 、 nicotinamide adenine dinucleotide 生成 2-dehydro-D-erythronate 、 氢(+1)阳离子 、 NADH
  参考文献：
  名称：

  Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars

  摘要：

  未知功能域（DUF）家族在Pfam数据库（版本29.0）的16,295个家族中占3,892个。鉴于它们的生物重要性，需要大规模的策略来完成它们的功能分配。在这里，我们阐述了一种综合的“基因组酶学”策略，以识别DUF1537家族（PF07005）中的多种功能。我们将高通量配体筛选结果与序列相似性网络和基因组邻域网络的协同分析相结合，以确定DUF1537家族的成员是新颖的ATP依赖性四碳糖激酶。这项研究说明了这种策略的实用性，并增加了我们对细菌碳水化合物代谢的了解。

  DOI：

  10.1073/pnas.1605546113
• 作为产物：
  描述：

  在 citrate synthase 、 acetyl-CoA synthetase 、 Agrobacterium tumefaciens C₅₈ recombinant Atu₃₂₆₆ protein 、 L-malate dehydrogenase 、 β-烟酰胺腺嘌呤二核苷酸 、 水 、 5’-三磷酸腺苷 、 辅酶 A 、 magnesium chloride 作用下， 生成 D-erythrononate
  参考文献：
  名称：

  Functional Annotation and Three-Dimensional Structure of an Incorrectly Annotated Dihydroorotase from cog3964 in the Amidohydrolase Superfamily

  摘要：

  The substrate specificities of two incorrectly annotated enzymes belonging to cog3964 from the amidohydrolase superfamily were determined. This group of enzymes are currently misannotated as either dihydroorotases or adenine deaminases. Atu3266 from Agrobacterium tumefaciens C58 and Oant2987 from Ochrobactrum anthropi ATCC 49188 were found to catalyze the hydrolysis of acetyl-(R)-mandelate and similar esters with values of K-cat/K-m that exceed 10(5) M-1 s(-1). These enzymes do not catalyze the deamination of adenine or the hydrolysis of dihydroorotate. Atu3266 was crystallized and the structure determined to a resolution of 2.62 angstrom. The protein folds as a distorted (beta/alpha)(8) barrel and binds two zincs in the active site. The substrate profile was determined via a combination of computational docking to the three-dimensional structure of Atu3266 and screening of a highly focused library of potential substrates. The initial weak hit was the hydrolysis of N-acetyl-D-serine (k(cat)/K-m = 4 M-1 s(-1)). This was followed by the progressive identification of acetyl-(R)-glycerate (k(cat)/K-m = 4 x 10(2) M-1 s(-1)), acetyl glycolate (k(cat)/K-m = 1.3 x 10(4) M-1 s(-1)), and ultimately acetyl-(R)-mandelate (k(cat)/K-m = 2.8 x 10(2) M-1 s(-1)).

  DOI：

  10.1021/bi301483z

文献信息

• Cyanohydrin synthesis: studies with carbon-13-labeled cyanide
  作者：Anthony S. Serianni、Hernan A. Nunez、Robert Barker

  DOI：10.1021/jo01304a038

  日期：1980.8
• Functional Annotation and Three-Dimensional Structure of an Incorrectly Annotated Dihydroorotase from cog3964 in the Amidohydrolase Superfamily
  作者：Argentina Ornelas、Magdalena Korczynska、Sugadev Ragumani、Desigan Kumaran、Tamari Narindoshvili、Brian K. Shoichet、Subramanyam Swaminathan、Frank M. Raushel

  DOI：10.1021/bi301483z

  日期：2013.1.8

  The substrate specificities of two incorrectly annotated enzymes belonging to cog3964 from the amidohydrolase superfamily were determined. This group of enzymes are currently misannotated as either dihydroorotases or adenine deaminases. Atu3266 from Agrobacterium tumefaciens C58 and Oant2987 from Ochrobactrum anthropi ATCC 49188 were found to catalyze the hydrolysis of acetyl-(R)-mandelate and similar esters with values of K-cat/K-m that exceed 10(5) M-1 s(-1). These enzymes do not catalyze the deamination of adenine or the hydrolysis of dihydroorotate. Atu3266 was crystallized and the structure determined to a resolution of 2.62 angstrom. The protein folds as a distorted (beta/alpha)(8) barrel and binds two zincs in the active site. The substrate profile was determined via a combination of computational docking to the three-dimensional structure of Atu3266 and screening of a highly focused library of potential substrates. The initial weak hit was the hydrolysis of N-acetyl-D-serine (k(cat)/K-m = 4 M-1 s(-1)). This was followed by the progressive identification of acetyl-(R)-glycerate (k(cat)/K-m = 4 x 10(2) M-1 s(-1)), acetyl glycolate (k(cat)/K-m = 1.3 x 10(4) M-1 s(-1)), and ultimately acetyl-(R)-mandelate (k(cat)/K-m = 2.8 x 10(2) M-1 s(-1)).
• Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars
  作者：Xinshuai Zhang、Michael S. Carter、Matthew W. Vetting、Brian San Francisco、Suwen Zhao、Nawar F. Al-Obaidi、Jose O. Solbiati、Jennifer J. Thiaville、Valérie de Crécy-Lagard、Matthew P. Jacobson、Steven C. Almo、John A. Gerlt

  DOI：10.1073/pnas.1605546113

  日期：2016.7.19

  Domain of unknown function (DUF) families constitute 3,892 of the 16,295 families in the Pfam database (release 29.0). Given their biological importance, large-scale strategies are required to accomplish their functional assignments. Here, we illustrate an integrated “genomic enzymology” strategy to identify diverse functions within the DUF1537 family (PF07005). We combined high-throughput ligand screening results for transport system solute binding proteins with the synergetic analysis of sequence similarity networks and genome neighborhood networks to establish that the members of the DUF1537 family are novel ATP-dependent four-carbon sugar kinases. This study illustrates the utility of this strategy and enhances our knowledge of bacterial carbohydrate catabolism.

  未知功能域（DUF）家族在Pfam数据库（版本29.0）的16,295个家族中占3,892个。鉴于它们的生物重要性，需要大规模的策略来完成它们的功能分配。在这里，我们阐述了一种综合的“基因组酶学”策略，以识别DUF1537家族（PF07005）中的多种功能。我们将高通量配体筛选结果与序列相似性网络和基因组邻域网络的协同分析相结合，以确定DUF1537家族的成员是新颖的ATP依赖性四碳糖激酶。这项研究说明了这种策略的实用性，并增加了我们对细菌碳水化合物代谢的了解。