[(1R)-5-amino-1-carboxypentyl]azanium

• 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: [(1R)-5-amino-1-carboxypentyl]azanium
• 化学式: C6H15N2O2+
• 分子量: 147.2
• InChiKey: KDXKERNSBIXSRK-RXMQYKEDSA-O

计算性质

• 辛醇/水分配系数(LogP)：
  -2.4
• 重原子数：
  10
• 可旋转键数：
  4
• 环数：
  0.0
• sp3杂化的碳原子比例：
  0.83
• 拓扑面积：
  95.4
• 氢给体数：
  2
• 氢受体数：
  2

反应信息

• 作为反应物：
  描述：

  [(1R)-5-amino-1-carboxypentyl]azanium 生成 (2R,5S)-2,5-Diaminohexanoate
  参考文献：
  名称：

  Identification of a Novel Pyridoxal 5‘-Phosphate Binding Site in Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase from Porphyromonas gingivalis

  摘要：

  Lysine 5,6-aminomutase (5,6-LAM) catalyzes the interconversion of D-lysine with 2,5-diaminohexanoate and of L-beta-lysine with 3,5-diaminohexanoate. The coenzymes for 5,6-LAM are adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP). In the proposed chemical mechanism, AdoCbl initiates the formation of substrate radicals, and PLP facilitates the radical rearrangement by forming an external aldimine linkage with the E-amino group of a substrate, either D-lysine or L-beta-lysine. In the resting enzyme, an internal aldimine between PLP and an essential lysine in the active site facilitates productive PLP binding and catalysis. We present here biochemical, biophysical, and site-directed mutagenesis experiments, which document the existence of an essential lysine residue in the active site of 5,6-LAM from Porphyromonas gingivalis. Reduction of 5,6-LAM with NaBH4 rapidly inactivates the enzyme and shifts the electronic absorption band from 420 to 325 nm. This is characteristic of the reduction of an aldimine linkage between the carbonyl group of PLP and the E-amino group of a lysine residue. The reduced peptide was identified by Q-TOF/MS and further confirmed by Q-TOF/MS/MS sequencing. We show that lysine 144 in the small subunit of 5,6-LAM is the essential lysine residue. Lysine 144(beta) is separated by only 11 amino acids from histidine 133(beta), which forms a part of the "base-off"-AdoCbl binding motif. The sequence of the novel PLP-binding motif is conserved in 5,6-LAM from Clostridium sticklandii and P. gingivalis, and it is distinct from all known PLP-binding motifs. Mutation of lysine 144(beta) to glutamine led to K144Q(beta)-5,6-LAM, which displayed no enzymatic activity and no absorption band corresponding to an internal PLP-aldamine. In summary, we introduce a novel PLP-binding motif, the first to be discovered in an AdoCbl-dependent enzyme.

  DOI：

  10.1021/bi020255k
• 作为产物：
  描述：

  H-Lys-OH 生成 [(1R)-5-amino-1-carboxypentyl]azanium
  参考文献：
  名称：

  假单胞菌假单胞菌的周质，吡ido醛-5'-磷酸依赖性氨基酸消旋酶。

  摘要：

  吡ido醛5'-磷酸（PLP）依赖性氨基酸消旋体几乎在每种细菌中都存在，但底物特异性可能有很大差异。我们在这里通过经典方法从大肠杆菌中分离了大假单胞菌的克隆的广泛底物特异性消旋酶ArgR。该消旋酶具有生化特性，除其他方面外，已证实其主要对赖氨酸，精氨酸和鸟氨酸具有活性，而对丙氨酸仅具有弱活性，而经过比较研究的同一生物的丙氨酸消旋酶仅对丙氨酸起作用。出乎意料的是，对ArgR的氨基末端进行测序揭示了蛋白质的加工过程，信号肽被切割掉了。随后的定位研究表明，taetrolens和E. 大肠杆菌ArgR活性几乎只存在于周质中，这一特征迄今为止对于任何氨基酸消旋酶都未知。制备了带有羧基末端His-tag的ArgR衍生物，这被证明甚至可以定位在周质中缺乏双精氨酸易位（Tat）途径的大肠杆菌突变体中。这些数据表明，ArgR被合成为前肽，并以与Tat无关的方式易位。因此，我们建议ArgR易位取决于Sec系统

  DOI：

  10.1007/s00253-009-1942-7

文献信息

• Identification of the Initial Steps in <scp>d</scp> -Lysine Catabolism in <i>Pseudomonas putida</i>
  作者：Olga Revelles、Rolf-Michael Wittich、Juan L. Ramos

  DOI：10.1128/jb.01538-06

  日期：2007.4

  Pseudomonas putida uses l -lysine as the sole carbon and nitrogen source which preferentially requires its metabolism through two parallel pathways. In one of the pathways δ-aminovalerate is the key metabolite, whereas in the other l -lysine is racemized to d -lysine, and l -pipecolate and α-aminoadipate are the key metabolites. All the genes and enzymes involved in the d -lysine pathway, except for those involved in the conversion of d -lysine into Δ ¹ -piperideine-2-carboxylate, have been identified previously (30). In this study we report that the conversion of d -lysine into Δ ¹ -piperideine-2-carboxylate can be mediated by a d -lysine aminotransferase (PP3590) and a d -lysine dehydrogenase (PP3596). From a physiological point of view PP3596 plays a major role in the catabolism of d -lysine since its inactivation leads to a marked reduction in the growth rate with l - or d -lysine as the sole carbon and nitrogen source, whereas inactivation of PP3590 leads only to slowed growth. The gene encoding PP3590, called here amaC , forms an operon with dpkA , the gene encoding the enzyme involved in conversion of Δ ¹ -piperideine-2-carboxylate to l -pipecolate in the d -lysine catabolic pathway. The gene encoding PP3596, called here amaD , is the fifth gene in an operon made up of seven open reading frames (ORFs) encoding PP3592 through PP3597. The dpkA amaC operon was transcribed divergently from the operon ORF3592 to ORF3597. Both promoters were mapped by primer extension analysis, which showed that the divergent −35 hexamers of these operon promoters were adjacent to each other. Transcription of both operons was induced in response to l - or d -lysine in the culture medium.

  摘要 假单胞菌 使用 l -赖氨酸作为唯一的碳源和氮源，因此需要通过两条平行途径进行代谢。在其中一条途径中，δ-氨基戊酸是关键的代谢产物，而在另一条途径中，l-赖氨酸是关键的代谢产物。 l -赖氨酸消旋化为 d -赖氨酸，以及 l -哌啶酸和α-氨基己二酸是关键的代谢产物。参与 d -赖氨酸外消旋化的所有基因和酶 d -赖氨酸途径中的所有基因和酶，除了参与转化 d d -赖氨酸转化为 Δ 1 -哌啶-2-羧酸盐的过程外，其他过程均已确定（30）。在这项研究中，我们报告了 d -赖氨酸转化为 Δ 1 -哌啶-2-羧酸盐的转化可由一个 d -赖氨酸氨基转移酶（PP3590）和 d -赖氨酸脱氢酶（PP3596）介导。从生理学的角度来看，PP3596 在 d -赖氨酸的分解代谢中发挥着重要作用。 d -赖氨酸的分解代谢中起着重要作用，因为它的失活会导致生长速度明显降低。 l - 或 d -赖氨酸作为唯一碳源和氮源时，生长速度会明显降低，而 PP3590 失活只会导致生长速度减慢。编码 PP3590 的基因在这里称为 amaC 与 dpkA 形成一个操作子，该基因编码参与Δ1 和Δ2 转化的酶。 1 -哌啶-2-羧酸转化为 l 哌啶-2-甲酸转化为 l d -赖氨酸的代谢途径。编码 PP3596 的基因在这里称为 amaD 是由编码 PP3592 至 PP3597 的七个开放阅读框（ORF）组成的操作子中的第五个基因。其 dpkA amaC 操作子 ORF3592 至 ORF3597 的转录分化。通过引物延伸分析绘制了这两个启动子的图谱，结果表明这两个操作子启动子的-35六聚体彼此相邻。这两个操作子的转录都是在以下条件下被诱导的 l - 或 d -赖氨酸诱导两个操作子的转录。
• Construction and Properties of a Fragmentary D-Amino Acid Aminotransferase
  作者：Y. Fuchikami、T. Yoshimura、A. Gutierrez、K. Soda、N. Esaki

  DOI：10.1093/oxfordjournals.jbchem.a022206

  日期：1998.11.1

  D-Amino acid aminotransferase [EC 2.6.1.21] catalyzes the inter-conversion between various D-amino acids and alpha-keto acids. The subunit of the homodimeric enzyme from Bacillus sp. YM-1 consists of two domains connected by a single loop, which has no direct contact with the active site residues or the cofactor, pyridoxal 5'-phosphate [Sugio, S., Petsko, G.A., Manning, J.M., Soda, K., and Ringe, D

  D-氨基酸氨基转移酶[EC 2.6.1.21]催化各种D-氨基酸和α-酮酸之间的相互转化。来自芽孢杆菌属的同二聚酶的亚基。YM-1由通过单环连接的两个域组成，该环与活性位点残基或辅因子吡ido醛5'-磷酸[Sugio，S.，Petsko，GA，Manning，JM，Soda，K. ，和Ringe，D。（1995）Biochemistry 34，9661-9669]。我们构建了两个质粒，一个质粒编码对应于N端结构域的多肽片段，另一个编码对应于C端结构域的片段。当两个多肽片段在同一宿主细胞中一起表达时，产生了由两组两个多肽片段组成的活性片段酶。当两个多肽片段分别表达时，他们每个人都提供了可溶性蛋白，但没有活性。然而，在两个片段的混合物孵育后，D-氨基酸氨基转移酶活性出现。将活性片段酶纯化至均质并进行表征；除了底物特异性，α-酮戊二酸的抑制作用和热稳定性外，在各种酶学性质上与野生型酶相似。与野生
• STM2360 encodes a d-ornithine/d-lysine decarboxylase in Salmonella enterica serovar typhimurium
  作者：Robert S. Phillips、Pafe Poteh、Katherine A. Miller、Timothy R. Hoover

  DOI：10.1016/j.abb.2017.09.010

  日期：2017.11

  decarboxylase (DOKDC). The reaction products, cadaverine and putrescine, respectively, were identified by NMR and mass spectrometry. The substrate specificity of DOKDC is d-Lysine > d-Ornithine. This is the first pyridoxal-5′-phosphate dependent decarboxylase identified to act on d-amino acids. STM2358, located in the same operon, has ornithine racemase activity. This suggests that the physiological

  STM2360是位于肠炎沙门氏菌血清鼠伤寒沙门氏菌LT2中一个功能不确定的小操纵子中的基因。所述的STM2360节目显著相似性（约30％同一性），以二氨基庚二酸脱羧酶（DapDC），参与一个折III的吡哆醛-5'-磷酸（PLP）依赖性酶的氨基酸序列升赖氨酸的生物合成。我们已经发现，由STM2360编码的蛋白质具有以前未记录的催化活性，即d-鸟氨酸/ d-赖氨酸脱羧酶（DOKDC）。通过NMR和质谱分别鉴定了反应产物尸胺和腐胺。DOKDC的底物特异性为d-赖氨酸>  d-鸟氨酸。这是第一个被鉴定为对d-氨基酸起作用的依赖吡ido醛5'-磷酸的脱羧酶。位于同一操纵子中的STM2358具有鸟氨酸消旋酶活性。这表明脱羧酶和操纵子的生理底物是鸟氨酸。具有高序列同一性的STM2360同源物（> 80％）在其他常见肠细菌中发现，包括物种克雷伯氏菌，柠檬酸杆菌属，弧菌属和哈夫尼菌属，以及梭菌在厚壁菌门，和假单胞菌属。
• Structural basis for the broad specificity of a new family of amino-acid racemases
  作者：Akbar Espaillat、César Carrasco-López、Noelia Bernardo-García、Natalia Pietrosemoli、Lisandro H. Otero、Laura Álvarez、Miguel A. de Pedro、Florencio Pazos、Brigid M. Davis、Matthew K. Waldor、Juan A. Hermoso、Felipe Cava

  DOI：10.1107/s1399004713024838

  日期：2014.1.1

  Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical D-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be appreciated. Here, extensive crystallographic, mutational, biochemical and bioinformatic studies were used to define the molecular features of the racemase BsrV that enable this enzyme to accommodate more diverse substrates than the related PLP-dependent alanine racemases. Conserved residues were identified that distinguish BsrV and a newly defined family of broad-spectrum racemases from alanine racemases, and these residues were found to be key mediators of the multispecificity of BrsV. Finally, the structural analysis of an additional Bsr that was identified in the bioinformatic analysis confirmed that the distinguishing features of BrsV are conserved among Bsr family members.
• Radical Triplets and Suicide Inhibition in Reactions of 4-Thia-<scp>d</scp>- and 4-Thia-<scp>l</scp>-lysine with Lysine 5,6-Aminomutase
  作者：Kuo-Hsiang Tang、Steven O. Mansoorabadi、George H. Reed、Perry A. Frey

  DOI：10.1021/bi900828f

  日期：2009.9.1

  Lysine 5,6-aminomutase (5,6-LAM) catalyzes the interconversions of D- or L-lysine and the corresponding enantiomers of 2,5-diaminohexanoate, as well as the interconversion of L-beta-lysine and L-3,5-diaminohexanoate. The reactions of 5,6-LAM are 5'-deoxyadenosylcobalamin- and pyridoxal-5'-phosphate (PLP)-dependent. Similar to other 5'-deoxyadenosylcobalamin-dependent enzymes, 5,6-LAM is thought to function by a radical mechanism. No free radicals can be detected by electron paramagnetic resonance (EPR) spectroscopy In reactions of 5,6-LAM With D- or L-lysine or With L-beta-lysine. However, the substrate analogues 4-thia-L-lysine and 4-thia-D-lysine undergo early steps in the mechanism to form two radical species that are readily detected by EPR spectroscopy. Cob(II)alamin and 5'-deoxyadenosine derived from 5'-deoxyadenosylcobalamin are also detected. The radicals are proximal to and spin-coupled with low-spin Co2+ in cob(II)alamin and appear as radical triplets. The radicals are reversibly formed but do not proceed to stable products, so that 4-thia-D- and L-lysine are suicide inhibitors. Inhibition attains equilibrium between the active Michaelis complex and the inhibited radical triplets. The structure of the transient 4-thia-L-lysine radical is analogous to that of the first substrate-related radical in the putative isomerization mechanism. The second, persistent radical is more stable than the transient species and is assigned as a tautomer, in which a C6(H) of the transient radical is transferred to the carboxaldehyde carbon (C4') of PLP. The. persistent radical blocks the active site and inhibits the enzyme, but it decomposes very slowly at <= 1% of the rate of formation to regenerate the active enzyme. Fundamental differences between reversible suicide inactivation by 4-thia-D- or L-4-lysine and irreversible suicide inactivation by D- or L-lysine are discussed, The observation of the transient radical supports the hypothetical isomerization mechanism.