D-ornithinium(1+)

• 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: D-ornithinium(1+)
• 英文别名: (2R)-2,5-bis(azaniumyl)pentanoate
• 化学式: C5H13N2O2+
• 分子量: 133.17
• InChiKey: AHLPHDHHMVZTML-SCSAIBSYSA-O

计算性质

• 辛醇/水分配系数(LogP)：
  -3.8
• 重原子数：
  9
• 可旋转键数：
  3
• 环数：
  0.0
• sp3杂化的碳原子比例：
  0.8
• 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：

  D-ornithinium(1+) 生成 (2R,4S)-2,4-diazaniumylpentanoate
  参考文献：
  名称：

  粘液梭状芽胞杆菌依赖腺苷钴胺素的D-鸟氨酸氨基变位酶的克隆，测序，异源表达，纯化和鉴定。

  摘要：

  来自粘梭菌的D-鸟氨酸氨基变位酶催化D-鸟氨酸向（2R，4S）-2,4-二氨基戊酸的可逆重排。编码d-鸟氨酸氨基变位酶的两个基因已在大肠杆菌中克隆，测序和表达。oraS基因（编码具有121个氨基酸残基的蛋白具有M（r）12,800）位于oraE基因的上游，其编码具有753个氨基酸残基的蛋白具有M（r）82,900。全酶似乎包含α（2）β（2）-异四聚体。OraS与Swiss-Prot数据库中的其他蛋白质没有明显的同源性。OraE推导的氨基酸序列包括保守的碱基间隔/组氨酸上的钴胺素结合基序DXHXXG。OraE在大肠杆菌中表达为包涵体。在OraE上进行重折叠实验表明，OraS和OraE之间的相互作用以及磷酸吡ido醛或腺苷钴胺素的结合在重折叠过程中起着重要作用。d-鸟氨酸，5'-脱氧腺苷钴胺素（AdoCbl）和吡ido醛5'-磷酸酯（PLP）的K（m）值分别为44.5 +/- 2.8、0.43

  DOI：

  10.1074/jbc.m108365200
• 作为产物：
  描述：

  L-ornithinium(1+) 生成 D-ornithinium(1+)
  参考文献：
  名称：

  棒状梭状芽孢杆菌鸟氨酸消旋酶的纯化和性质。

  摘要：

  如十二烷基硫酸钠-聚丙烯酰胺凝胶电泳所示，鸟氨酸消旋酶已从粘梭菌纯化至同质。这是已知对鸟氨酸高度特异的第一个消旋酶。这种PLP依赖性酶的M（r）为92，000，L-鸟氨酸的K（m）为0.77 +/- 0.05 mM，ak（cat）为980 +/- 20 s（-1）。

  DOI：

  10.1128/jb.182.7.2052-2054.2000

文献信息

• Role of histidine 225 in adenosylcobalamin-dependent ornithine 4,5-aminomutase
  作者：Caitlyn Makins、François N. Miros、Nigel S. Scrutton、Kirsten R. Wolthers

  DOI：10.1016/j.bioorg.2011.08.003

  日期：2012.2

  inactivation. pH-dependence studies show that kcat increases with the ionization of a functional group, but it is not attributed to His225. Binding of 2,4-diaminobutyric acid to native OAM leads to formation of an overstabilized 2,4-diaminobutyryl–PLP derived radical. In the H225A and the H225Q mutants, the radical forms and then decays, as evidenced by accumulation of cob(III)alamin. From these data, we propose

  吡哆醛5'-磷酸（PLP），鸟氨酸4,5-氨基变位酶（OAM）的活性位点，形成席夫碱与N- δ所述的d鸟氨酸侧链和促进氨基酸的互变至（2 - [R ，4 S ) 2,4-二氨基戊酸通过基于自由基的机制。OAM的晶体结构表明，His225是将PLP酚氧氢键距离内，并可能影响的pK一个自由基重排过程中希夫碱的形成。为了评估 His225 在自由基稳定和催化中的作用，将残基替换为谷氨酰胺和丙氨酸。H225Q 和 H225A 变体的催化转化率分别降低了 3 倍和 10 倍，催化效率降低（两种突变体均降低了 7 倍）。催化性能下降与导致酶失活的基于自由基的副反应的增加无关。pH 依赖性研究表明k cat随官能团的电离而增加，但不归因于 His225。2,4-二氨基丁酸与天然 OAM 的结合导致形成过度稳定的 2,4-二氨基丁酰基-PLP 衍生自由基。在 H225A 和 H225Q 突变体中，自由基形成然后衰变，如
• Cloning, Sequencing, Heterologous Expression, Purification, and Characterization of Adenosylcobalamin-dependentd-Ornithine Aminomutase from Clostridium sticklandii
  作者：Hao-Ping Chen、Shih-Hsiung Wu、Ya-Lin Lin、Chih-Ming Chen、San-San Tsay

  DOI：10.1074/jbc.m108365200

  日期：2001.11

  D-Ornithine aminomutase from Clostridium sticklandii catalyzes the reversible rearrangement of d-ornithine to (2R,4S)-2,4-diaminopentanoic acid. The two genes encoding d-ornithine aminomutase have been cloned, sequenced, and expressed in Escherichia coli. The oraS gene, which encodes a protein of 121 amino acid residues with M(r) 12,800, is situated upstream of the oraE gene, which encodes a protein

  来自粘梭菌的D-鸟氨酸氨基变位酶催化D-鸟氨酸向（2R，4S）-2,4-二氨基戊酸的可逆重排。编码d-鸟氨酸氨基变位酶的两个基因已在大肠杆菌中克隆，测序和表达。oraS基因（编码具有121个氨基酸残基的蛋白具有M（r）12,800）位于oraE基因的上游，其编码具有753个氨基酸残基的蛋白具有M（r）82,900。全酶似乎包含α（2）β（2）-异四聚体。OraS与Swiss-Prot数据库中的其他蛋白质没有明显的同源性。OraE推导的氨基酸序列包括保守的碱基间隔/组氨酸上的钴胺素结合基序DXHXXG。OraE在大肠杆菌中表达为包涵体。在OraE上进行重折叠实验表明，OraS和OraE之间的相互作用以及磷酸吡ido醛或腺苷钴胺素的结合在重折叠过程中起着重要作用。d-鸟氨酸，5'-脱氧腺苷钴胺素（AdoCbl）和吡ido醛5'-磷酸酯（PLP）的K（m）值分别为44.5 +/- 2.8、0.43
• D-Arginase of Arthrobacter sp. KUJ 8602: Characterization and Its Identity with Zn2+-Guanidinobutyrase
  作者：N. Arakawa

  DOI：10.1093/jb/mvg016

  日期：2003.1.1

  d-Arginase activity was found in the cells of an isolate, Arthrobacter sp. KUJ 8602, grown in the l-arginine medium, and the enzyme was purified and characterized. Its molecular weight was estimated to be about 232,000 by gel filtration, and that of the subunit was approximately 40,000 by SDS-PAGE, suggesting that the enzyme is a homohexamer. The enzyme acted on not only d-arginine but also 4-guanidinobutyrate, 3-guanidinopropionate and even l-arginine. The Vmax/Km values for 4-guanidinobutyrate and d-arginine were determined to be 87 and 0.81 µmol/min/mg/mM, respectively. Accordingly, the enzyme is regarded as a kind of guanidinobutyrase [EC 3.5.3.7]. The pH optima for 4-guanidinobutyrate and d-arginine were 9.0 and 9.5, respectively. The enzyme was inhibited competitively by 5-aminovalerate, and thiol carboxylates such as mercaptoacetate served as strong mixed-type inhibitors. The enzyme contained about 1 g-atom of firmly bound Zn2+ per mol of subunit, and removal of the metal ions by incubation with 1,10-phenanthroline resulted in loss of activity. The inactivated enzyme was reactivated markedly by incubation with either Zn2+ or Co2+, and slightly by incubation with Mn2+. The nucleotide sequence of enzyme contains an open reading frame that encodes a polypeptide of 353 amino acid residues (Mr: 37,933). The predicted amino acid sequence contains sequences involved in the binding of metal ions and the guanidino group of the substrate, which show a high homology with corresponding sequences of Mn2+-dependent amidinohydrolases such as agmatinase from Escherichia coli and l-arginase from rat liver, though the homology of their entire sequences is relatively low (24–43%).

  not yet确定。
• 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。
• Identification and Characterization of the <i>Staphylococcus aureus</i> Gene Cluster Coding for Staphyloferrin A
  作者：Jennifer L. Cotton、Jianshi Tao、Carl J. Balibar

  DOI：10.1021/bi801844c

  日期：2009.2.10

  the ability to synthesize the siderophore, we reconstituted staphyloferrin A biosynthesis in vitro by expressing and purifying two key enzymes in the pathway. As with other polycarboxylate siderophores, staphyloferrin A is biosynthesized using the recently described nonribosomal peptide synthetase independent siderophore (NIS) biosynthetic pathway. Two NIS synthetases condense two molecules of citric

  铁载体是允许细菌在铁限制环境中生长的关键毒力因子。已知革兰氏阳性病原体金黄色葡萄球菌会产生四种铁载体，其遗传和/或结构数据尚不清楚。在这里，我们表征了负责产生普遍的铁载体葡萄球菌铁蛋白A的基因簇。除了在异源宿主大肠杆菌中表达该簇，赋予了合成铁载体的能力外，我们在体外还重建了葡萄球菌铁蛋白A的生物合成。通过表达和纯化途径中的两种关键酶。与其他多羧酸盐铁载体一样，葡萄铁蛋白A是使用最近描述的非核糖体肽合成酶非依赖性铁载体（NIS）生物合成途径进行生物合成的。两个NIS合成酶以δ-胺为亲核试剂，通过SfnaD逐步将两个柠檬酸分子缩合为d-鸟氨酸，以形成第一个酰胺，随后是SfnaB，利用α-胺完成金黄色铁蛋白A的合成。