CMP-3-deoxy-beta-D-manno-octulosonate(2-)

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘧啶核苷酸
• 英文名称: CMP-3-deoxy-beta-D-manno-octulosonate(2-)
• 英文别名: (2R,4R,5R,6R)-2-[[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-oxidophosphoryl]oxy-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylate
• 化学式: C17H24N3O15P-2
• 分子量: 541.4
• InChiKey: YWWJKULNWGRYAS-UOVSKDHASA-L

计算性质

• 辛醇/水分配系数(LogP)：
  -5.6
• 重原子数：
  36
• 可旋转键数：
  8
• 环数：
  3.0
• sp3杂化的碳原子比例：
  0.71
• 拓扑面积：
  297
• 氢给体数：
  7
• 氢受体数：
  15

反应信息

• 作为反应物：
  描述：

  (KDO)2-lipid IVA(6-) 、 CMP-3-deoxy-beta-D-manno-octulosonate(2-) 生成 (KDO)3-lipid IVA(7-) 、 cytidine 5'-monophosphate 、 氢(+1)阳离子
  参考文献：
  名称：

  Comparative analyses of secondary gene products of 3-deoxy-D-manno-oct-2-ulosonic acid transferases from Chlamydiaceae in Escherichia coli K-12

  摘要：

  The waaA gene encoding the essential, lipopolysaccharide (LPS)‐specific 3‐deoxy‐dmanno‐oct‐2‐ulosonic acid (Kdo) transferase was inactivated in the chromosome of a heptosyltransferase I and II deficient Escherichia coli K‐12 strain by insertion of gene expression cassettes encoding the waaA genes of Chlamydia trachomatis, Chlamydophila pneumoniae or Chlamydophila psittaci. The three chlamydial Kdo transferases were able to complement the knockout mutation without changing the growth or multiplication behaviour. The LPS of the mutants were serologically and structurally characterized in comparison to the LPS of the parent strain using compositional analyses, high performance anion exchange chromatography, matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and specific monoclonal antibodies. The data show that chlamydial Kdo transferases can replace in E. coli K‐12 the host's Kdo transferase and retain the product specificities described in their natural background. In addition, we unequivocally proved that WaaA from C. psittaci transfers predominantly four Kdo residues to lipid A, forming a branched tetrasaccharide with the structure α‐Kdo‐(2→8)‐[α‐Kdo‐(2→4)]‐α‐Kdo‐(2→4)‐α‐Kdo.

  DOI：

  10.1046/j.1432-1327.2000.01619.x
• 作为产物：
  描述：

  3-deoxy-alpha-D-manno-oct-2-ulosonate 、 cytidine 5'-triphosphate 生成 CMP-3-deoxy-beta-D-manno-octulosonate(2-) 、 pyrophosphoric acid
  参考文献：
  名称：

  Catalytic Mechanism of CMP:2-Keto-3-deoxy-manno-octonic Acid Synthetase As Derived from Complexes with Reaction Educt and Product^,

  摘要：

  The activation of the sugar 2-keto-3-deoxy-manno-octonic acid (Kdo) is catalyzed by CMP-Kdo synthetase (EC 2.7.7.38) and results in a monophosphate diester with CMP. The enzyme is a pharmaceutical target because CMP-Kdo is required for the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. We have established the structures of an enzyme complex with the educt CTP and of a complex with the product CMP-Kdo by X-ray diffraction analyses at 100 K, both at 2.6 A resolution. The N-terminal domains of the dimeric enzyme bind CTP in a peculiar nucleotide-binding fold with the beta- and gamma-phosphates located at the so-called "PP-loop", whereas the C-terminal domains participate in Kdo binding and in the dimer interface. The unstable nucleotide-sugar CMP-Kdo was produced in a crystal and stabilized by freezing to 100 K. Its formation is accompanied by an induced fit involving mainchain displacements in the 2 A range. The observed binding conformations together with the amino acid conservation pattern during evolution and the putative location of the required Mg(2+) ion suggest a reaction pathway. The enzyme is structurally homologous to the CMP-N-acetylneuraminic acid synthetases in all parts except for the dimer interface. Moreover, the chainfold and the substrate-binding positions resemble those of other enzymes processing nucleotide sugars.

  DOI：

  10.1021/bi0119060

文献信息

• Structural and mechanistic analysis of the membrane-embedded glycosyltransferase WaaA required for lipopolysaccharide synthesis
  作者：Helgo Schmidt、Guido Hansen、Sonia Singh、Anna Hanuszkiewicz、Buko Lindner、Koichi Fukase、Ronald W. Woodard、Otto Holst、Rolf Hilgenfeld、Uwe Mamat、Jeroen R. Mesters

  DOI：10.1073/pnas.1119894109

  日期：2012.4.17

  WaaA is a key enzyme in the biosynthesis of LPS, a critical component of the outer envelope of Gram-negative bacteria. Embedded in the cytoplasmic face of the inner membrane, WaaA catalyzes the transfer of 3-deoxy- d - manno -oct-2-ulosonic acid (Kdo) to the lipid A precursor of LPS. Here we present crystal structures of the free and CMP-bound forms of WaaA from Aquifex aeolicus , an ancient Gram-negative hyperthermophile. These structures reveal details of the CMP-binding site and implicate a unique sequence motif (GGS/TX ₅ GXNXLE) in Kdo binding. In addition, a cluster of highly conserved amino acid residues was identified which represents the potential membrane-attachment and acceptor-substrate binding site of WaaA. A series of site-directed mutagenesis experiments revealed critical roles for glycine 30 and glutamate 31 in Kdo transfer. Our results provide the structural basis of a critical reaction in LPS biosynthesis and allowed the development of a detailed model of the catalytic mechanism of WaaA.

  WaaA是LPS生物合成的关键酶，LPS是革兰氏阴性细菌外层包膜的重要组成部分。WaaA嵌入在内膜的胞质面上，催化3-去氧- d - 曼 -八烯酸（Kdo）向LPS的脂多糖前体转移。本研究展示了来自古老的革兰氏阴性超热嗜水气单胞菌Aquifex aeolicus的WaaA的自由和CMP结合形式的晶体结构。这些结构揭示了CMP结合位点的细节，并暗示Kdo结合中存在一个独特的序列基序（GGS/TX ₅ GXNXLE）。此外，还确定了一簇高度保守的氨基酸残基，代表WaaA的潜在膜附着和受体底物结合位点。一系列定点突变实验揭示了甘氨酸30和谷氨酸31在Kdo转移中的关键作用。我们的结果提供了LPS生物合成中关键反应的结构基础，并允许开发WaaA催化机制的详细模型。
• A Mono-functional 3-Deoxy-d-manno-octulosonic Acid (Kdo) Transferase and a Kdo Kinase in Extracts of Haemophilus influenzae
  作者：Kimberly A. White、Igor A. Kaltashov、Robert J. Cotter、Christian R.H. Raetz

  DOI：10.1074/jbc.272.26.16555

  日期：1997.6

  influenzae contains a single 3-deoxy-D-manno-octulosonic acid (Kdo) residue, linked to the 6' position of lipid A. In Escherichia coli and related organisms, a Kdo disaccharide is attached to lipid A. In previous studies, we cloned the gene (kdtA) encoding the E. coli Kdo transferase and demonstrated that homogeneous preparations of KdtA polypeptide catalyzed the attachment of both Kdo groups to the precursor

  流感嗜血杆菌的脂多糖含有一个单一的3-deoxy-D-manno-octulosonic acid（Kdo）残基，与脂质A的6'位置相连。在大肠杆菌和相关生物中，Kdo二糖附着在脂质A上。在研究中，我们克隆了编码大肠杆菌Kdo转移酶的基因（kdtA），并证明KdtA多肽的均质制剂可催化两个Kdo基团与前体脂质IVA的结合。大肠杆菌KdtA仅产生痕量的单糖基化产物。现在我们表明，单个Kdo被转移至流感嗜血杆菌提取物中的脂质IVA。流感嗜血杆菌的单功能Kdo转移酶是膜结合的，并且反应依赖于CMP-Kdo生成系统，例如在大肠杆菌中。在H中，Kdo转移至脂质IVA的比活性为0.5-1 nmol / min / mg。流感膜。利用溶解的流感嗜血杆菌膜，制备毫克量的Kdo-脂质IVA用于分析。基质辅助激光解吸/电离质谱分析显示，母体离子（MH）-的m / z 1626.0，与添加单个Kdo部分一致。像
• <i>Bordetella pertussis waaA</i>Encodes a Monofunctional 2-Keto-3-Deoxy-<scp>d</scp>-<i>manno</i>-Octulosonic Acid Transferase That Can Complement an<i>Escherichia coli waaA</i>Mutation
  作者：Tomoko Isobe、Kimberley A. White、Andrew G. Allen、Michael Peacock、Christian R. H. Raetz、Duncan J. Maskell

  DOI：10.1128/jb.181.8.2648-2651.1999

  日期：1999.4.15

  Bordetella pertussislipopolysaccharide (LPS) contains a single 2-keto-3-deoxy-d-manno-octulosonic acid (Kdo) residue, whereas LPS fromEscherichia colicontains at least two. Here we report thatB. pertussis waaAencodes an enzyme capable of transferring only a single Kdo during the biosynthesis of LPS and that this activity is sufficient to complement anE. coli waaAmutation.

  摘要百日咳杆菌脂多糖（LPS）含有单个 2-酮基-3-脱氧-d-甘露辛二酸（Kdo）残基，而大肠埃希菌的 LPS 至少含有两个残基。在这里，我们报告了百日咳杆菌 waaA 编码的酶能够在 LPS 的生物合成过程中只转移一个 Kdo，而且这种活性足以补充大肠杆菌 waaA 突变。
• Structure of 3-deoxy-<i>manno</i>-octulosonate cytidylyltransferase from<i>Haemophilus influenzae</i>complexed with the substrate 3-deoxy-<i>manno</i>-octulosonate in the β-configuration
  作者：Hye-Jin Yoon、Min-Je Ku、Bunzo Mikami、Se Won Suh

  DOI：10.1107/s0907444908036342

  日期：2008.12.1

  The enzyme 3-deoxy-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase; CKS) catalyzes the activation of 3-deoxy-D-manno-octulosonate (or 2-keto-3-deoxy-manno-octonic acid; KDO) by forming CMP-KDO. CKS is unique to Gram-negative bacteria and is an attractive target for the development of antibacterial agents. The crystal structure of CKS from Haemophilus influenzae in complex with the substrate KDO has been determined at 2.30 A resolution by combining single-wavelength anomalous diffraction and molecular-replacement methods. The two monomers in the asymmetric unit differ in the conformation of their C-terminal alpha-helix (Ala230-Asn254). The KDO bound to the active site exists as the beta-pyranose form in the (5)C(2) chair conformation. The structure of CKS from H. influenzae in complex with KDO will be useful in structure-based inhibitor design.
• Ghalambor M.A.; Heath E.C., J Biol Chem, 1966, 0021-9258, 3216-21
  作者：Ghalambor M.A.、Heath E.C.

  DOI：——

  日期：——