(S)-2,3,4,5-tetrahydrodipicolinate

• 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: (S)-2,3,4,5-tetrahydrodipicolinate
• 英文别名: (2S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
• 化学式: C7H7NO4-2
• 分子量: 169.13
• InChiKey: CXMBCXQHOXUCEO-BYPYZUCNSA-L

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：
  92.6
• 氢给体数：
  0
• 氢受体数：
  5

反应信息

• 作为反应物：
  描述：

  (S)-2,3,4,5-tetrahydrodipicolinate 、 氢(+1)阳离子 、 水 生成 (S)-2-amino-6-oxopimelate
  参考文献：
  名称：

  Meso-alpha,epsilon-diaminopimelate D-dehydrogenase: distribution and the reaction product

  摘要：

  在测试的细菌中，发现Bacillus sphaericus，Brevibacterium sp.，Corynebacterium glutamicum和Proteus vulgaris的提取物中具有高活性的meso-alpha-epsilon-diaminopimelate脱氢酶。选择其中酶含量最丰富的B. sphaericus IFO 3525来研究酶反应。添加meso-alpha-epsilon-diaminopimelate到生长培养基中不能诱导该酶。反应产物被分离并鉴定为alpha-amino-epsilon-ketopimelate，通过在硅胶薄层色谱、吸收、红外和质子核磁共振光谱以及元素分析中与真实样品的2,4-二硝基苯肼酮的性质进行比较确定。酶促生成的alpha-amino-epsilon-ketopimelate可以被H2O2脱羧为L-alpha-aminoadipate，这表明底物中具有D构型的氨基基团被氧化脱氨化；该酶是D-氨基酸脱氢酶。L-alpha-Amino-epsilon-ketopimelate会自发脱水成环状的delta1-piperideine-2,6-dicarboxylate。该酶反应是可逆的，L-alpha-epsilon-ketopimelate的还原胺化会生成meso-alpha-epsilon-diaminopimelate。

  DOI：

  10.1128/jb.137.1.22-27.1979
• 作为产物：
  描述：

  (2R,6S)-2,6-diaminoheptanedioic acid 、 NADP⁺ 生成 (S)-2,3,4,5-tetrahydrodipicolinate 、 氢(+1)阳离子 、 NADPH(4-) 、 铵
  参考文献：
  名称：

  摘要：

  DOI：

文献信息

• Bacterial Distribution of the Use of Succinyl and Acetyl Blocking Groups in Diaminopimelic Acid Biosynthesis
  作者：Steven Weinberger、Charles Gilvarg

  DOI：10.1128/jb.101.1.323-324.1970

  日期：1970.1

  The use of acetate, rather than succinate, as a blocking group in diaminopimelate biosynthesis has been found only in species of the genus Bacillus .

  在二氨基戊二酸生物合成中使用乙酸酯作为阻断基团，而不是琥珀酸酯，发现只存在于芽孢杆菌属的物种中。
• Crystal Structure of ll-Diaminopimelate Aminotransferase from Arabidopsis thaliana: A Recently Discovered Enzyme in the Biosynthesis of l-Lysine by Plants and Chlamydia
  作者：Nobuhiko Watanabe、Maia M. Cherney、Marco J. van Belkum、Sandra L. Marcus、Mitchel D. Flegel、Matthew D. Clay、Michael K. Deyholos、John C. Vederas、Michael N.G. James

  DOI：10.1016/j.jmb.2007.05.061

  日期：2007.8

  inhibitors, the three-dimensional crystal structure of LL-DAP-AT was determined at 1.95 A resolution. The cDNA sequence of LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT) was optimized for expression in bacteria and cloned in Escherichia coli without its leader sequence but with a C-terminal hexahistidine affinity tag to aid protein purification. The structure of AtDAP-AT was determined using the multiple-wavelength

  细菌和植物中赖氨酸赖氨酸的基本生物合成途径是开发新型抗生素或除草剂的有吸引力的目标，因为人类中不存在这种赖氨酸，必须在饮食中获取该氨基酸。植物使用细菌通往L-赖氨酸的捷径，其中依赖吡al醛5'-磷酸（PLP）的酶ll-二氨基庚二酸酯氨基转移酶（LL-DAP-AT）将L-四氢二吡啶甲酸（L-THDP）直接转化为LL-DAP。此外，最近在衣原体中发现了LL-DAP-AT，这表明该酶的抑制剂也可能有效对抗这种生物。为了理解该酶的机理并协助抑制剂的设计，以1.95 A的分辨率确定了LL-DAP-AT的三维晶体结构。优化拟南芥LL-DAP-AT（AtDAP-AT）的cDNA序列，使其在细菌中表达，并克隆到大肠杆菌中而没有其前导序列，但具有C端六组氨酸亲和标签以帮助蛋白质纯化。使用硒代蛋氨酸衍生物的多波长异常色散（MAD）方法确定AtDAP-AT的结构。AtDAP-AT作为同型二聚体具有活性，每个亚基
• Biochemical and Phylogenetic Characterization of a Novel Diaminopimelate Biosynthesis Pathway in Prokaryotes Identifies a Diverged Form of <scp>ll</scp> -Diaminopimelate Aminotransferase
  作者：André O. Hudson、Charles Gilvarg、Thomas Leustek

  DOI：10.1128/jb.01381-07

  日期：2008.5

  A variant of the diaminopimelate (DAP)-lysine biosynthesis pathway uses an ll -DAP aminotransferase (DapL, EC 2.6.1.83) to catalyze the direct conversion of l -2,3,4,5-tetrahydrodipicolinate to ll -DAP. Comparative genomic analysis and experimental verification of DapL candidates revealed the existence of two diverged forms of DapL (DapL1 and DapL2). DapL orthologs were identified in eubacteria and archaea. In some species the corresponding dapL gene was found to lie in genomic contiguity with other dap genes, suggestive of a polycistronic structure. The DapL candidate enzymes were found to cluster into two classes sharing approximately 30% amino acid identity. The function of selected enzymes from each class was studied. Both classes were able to functionally complement Escherichia coli dapD and dapE mutants and to catalyze ll -DAP transamination, providing functional evidence for a role in DAP/lysine biosynthesis. In all cases the occurrence of dapL in a species correlated with the absence of genes for dapD and dapE representing the acyl DAP pathway variants, and only in a few cases was dapL coincident with ddh encoding meso -DAP dehydrogenase. The results indicate that the DapL pathway is restricted to specific lineages of eubacteria including the Cyanobacteria , Desulfuromonadales , Firmicutes , Bacteroidetes , Chlamydiae , Spirochaeta , and Chloroflexi and two archaeal groups, the Methanobacteriaceae and Archaeoglobaceae.

  摘要 二氨基亚硒酸盐(DAP)-赖氨酸生物合成途径的一个变体使用了一个 氨基转移酶 -DAP氨基转移酶（DAPL，EC 2.6.1.83）来催化 l-DAP-赖氨酸的直接转化。 l -2,3,4,5-四氢二羟酸直接转化为 -DAP。 -DAP。通过对候选 DAPL 的基因组比较分析和实验验证，发现存在两种不同形式的 DAPL（DAPL1 和 DAPL2）。在真细菌和古细菌中发现了 DAPL 的直向同源物。在某些物种中，相应的 DAPL 基因在基因组上与其他 DAP 基因在基因组中的连续性，表明存在多聚子结构。研究发现，DAPL 候选酶可分为两类，氨基酸相似度约为 30%。研究了每一类中选定酶的功能。两类酶都能对 大肠杆菌 DAPD 和 DAPE 突变体，并催化 -DAP转氨作用。 -DAP转氨作用，提供了在 DAP/赖氨酸生物合成中发挥作用的功能性证据。在所有情况下 DAPL 基因的缺失相关。 DAPD 和 DAPE 代表酰基 DAP 途径变体的基因的缺失相关，只有在少数情况下 DAPL 与 ddh 编码 中 -DAP脱氢酶。结果表明，DAPL 途径仅限于特定的真细菌系，包括 蓝藻 , 脱硫单胞菌 , 固态菌 , 类细菌 , 衣原体 , 螺旋体 和 和 和两个古菌类，即 甲烷杆菌科 和 古球菌科。
• An <scp>ll</scp>-Diaminopimelate Aminotransferase Defines a Novel Variant of the Lysine Biosynthesis Pathway in Plants
  作者：André O. Hudson、Bijay K. Singh、Thomas Leustek、Charles Gilvarg

  DOI：10.1104/pp.105.072629

  日期：2006.1.1

  Although lysine (Lys) biosynthesis in plants is known to occur by way of a pathway that utilizes diaminopimelic acid (DAP) as a central intermediate, the available evidence suggests that none of the known DAP-pathway variants found in nature occur in plants. A new Lys biosynthesis pathway has been identified in Arabidopsis (Arabidopsis thaliana) that utilizes a novel transaminase that specifically catalyzes the interconversion of tetrahydrodipicolinate and ll-diaminopimelate, a reaction requiring three enzymes in the DAP-pathway variant found in Escherichia coli. The ll-DAP aminotransferase encoded by locus At4g33680 was able to complement the dapD and dapE mutants of E. coli. This result, in conjunction with the kinetic properties and substrate specificity of the enzyme, indicated that ll-DAP aminotransferase functions in the Lys biosynthetic direction under in vivo conditions. Orthologs of At4g33680 were identified in all the cyanobacterial species whose genomes have been sequenced. The Synechocystis sp. ortholog encoded by locus sll0480 showed the same functional properties as At4g33680. These results demonstrate that the Lys biosynthesis pathway in plants and cyanobacteria is distinct from the pathways that have so far been defined in microorganisms.

  尽管植物中的赖氨酸（Lys）生物合成已知是通过利用二氨基戊二酸（DAP）作为中心中间体的途径进行的，但现有证据表明，在自然界中发现的已知DAP途径变体中，没有一种适用于植物。在拟南芥（拟南芥）中已经确定了一条新的Lys生物合成途径，该途径利用一种新型转氨酶，该转氨酶专门催化四氢双吡咯酸和ll-二氨基戊二酸之间的互变作用，这种反应需要Escherichia coli中发现的DAP途径变体中的三种酶。由位点At4g33680编码的ll-DAP氨基转移酶能够补充E. coli的DAPD和DAPE突变体。该酶的动力学性质和底物特异性，结合这一结果，表明ll-DAP氨基转移酶在体内条件下以Lys生物合成方向起作用。在所有已测序的蓝细菌物种中鉴定了At4g33680的同源物。由位点sll0480编码的Synechocystis sp.同源物表现出与At4g33680相同的功能特性。这些结果表明，植物和蓝细菌中的Lys生物合成途径与迄今为止在微生物中定义的途径不同。

• <scp>l</scp> , <scp>l</scp> -diaminopimelate aminotransferase, a trans-kingdom enzyme shared by <i>Chlamydia</i> and plants for synthesis of diaminopimelate/lysine
  作者：Andrea J. McCoy、Nancy E. Adams、André O. Hudson、Charles Gilvarg、Thomas Leustek、Anthony T. Maurelli

  DOI：10.1073/pnas.0608643103

  日期：2006.11.21

  The synthesis of meso -diaminopimelic acid ( m -DAP) in bacteria is essential for both peptidoglycan and lysine biosynthesis. From genome sequencing data, it was unclear how bacteria of the Chlamydiales order would synthesize m -DAP in the absence of dapD , dapC , and dapE , which are missing from the genome. Here, we assessed the biochemical capacity of Chlamydia trachomatis serovar L2 to synthesize m -DAP. Expression of the chlamydial asd , dapB , and dapF genes in the respective Escherichia coli m -DAP auxotrophic mutants restored the mutants to DAP prototrophy. Screening of a C. trachomatis genomic library in an E. coli Δ dapD DAP auxotroph identified ct390 as encoding an enzyme that restored growth to the Escherichia coli mutant. ct390 also was able to complement an E. coli Δ dapD Δ dapE , but not a Δ dapD Δ dapF mutant, providing genetic evidence that it encodes an aminotransferase that may directly convert tetrahydrodipicolinate to l , l -diaminopimelic acid. This hypothesis was supported by in vitro kinetic analysis of the CT390 protein and the fact that similar properties were demonstrated for the Protochlamydia amoebophila homologue, PC0685. In vivo , the C. trachomatis m -DAP synthesis genes are expressed as early as 8 h after infection. An aminotransferase activity analogous to CT390 recently has been characterized in plants and cyanobacteria. This previously undescribed pathway for m -DAP synthesis supports an evolutionary relationship among the chlamydiae, cyanobacteria, and plants and strengthens the argument that chlamydiae synthesize a cell wall despite the inability of efforts to date to detect peptidoglycan in these organisms.

  细菌中合成meso-二氨基戊二酸（m-DAP）对于肽聚糖和赖氨酸生物合成都是必不可少的。从基因组测序数据来看，不清楚衣原体目的菌序列中缺失的DAPD，DAPa href=https://www.molaid.com/MS_17084 target="_blank">PC和DAPE如何在没有这些基因的情况下合成m-DAP。在这里，我们评估了衣原体L2血清型合成m-DAP的生化能力。在相应的E. coli m-DAP辅助缺陷突变体中表达衣原体asd，DAPB和DAPF基因，可以使突变体恢复到DAP原核生物。在E. coli ΔDAPD DAP辅助缺陷突变体中筛选C. trachomatis基因组文库，发现ct390编码一种酶，可以使E. coli突变体恢复生长。ct390也能够补充E. coli ΔDAPD ΔDAPE，但不能补充ΔDAPD ΔDAPF突变体，为其编码一种氨基转移酶提供了遗传证据，该酶可能可以直接将四氢二异戊酸转化为L,L-二氨基戊二酸。CT390蛋白的体外动力学分析以及类似的特性也被证明在Protochlamydia amoebophila同源物PC0685中。在体内，C. trachomatis m-DAP合成基因在感染后8小时就开始表达。类似的氨基转移酶活性最近已在植物和蓝藻中进行了表征。这种以前未描述的m-DAP合成途径支持了衣原体、蓝藻和植物之间的进化关系，并加强了衣原体合成细胞壁的论点，尽管迄今为止无法在这些生物中检测到肽聚糖。