ADP-L-glycero-D-manno-heptose

• 分子结构分类: 有机化合物 - 核苷、核苷酸和类似物 - 嘌呤核苷酸
• 英文名称: ADP-L-glycero-D-manno-heptose
• 英文别名: ADP-L-glycero-beta-D-manno-heptose(2-)；[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-oxidophosphoryl] [(2S,3S,4S,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl] phosphate
• 化学式: C₁₇H₂₅N₅O₁₆P₂
• 分子量: 617.357
• InChiKey: KMSFWBYFWSKGGR-DTBZDYEHSA-L

计算性质

• 辛醇/水分配系数(LogP)：
  -7
• 重原子数：
  40
• 可旋转键数：
  10
• 环数：
  4.0
• sp3杂化的碳原子比例：
  0.71
• 拓扑面积：
  338
• 氢给体数：
  8
• 氢受体数：
  20

反应信息

• 作为反应物：
  描述：

  ADP-L-glycero-D-manno-heptose 、 在 L-lactate dehydrogenase 、 pyruvate kinase 、 Escherichia coli heptosyltransferase I 、 还原型辅酶Ⅰ 作用下， 生成 、 二磷酸腺苷
  参考文献：
  名称：

  Lipopolysaccharide Biosynthesis without the Lipids: Recognition Promiscuity ofEscherichia coliHeptosyltransferase I

  摘要：

  Heptosyltransferase I (HepI) is responsible for the transfer of L-glycero-D-manno-heptose to a 3-deoxy-alpha-D-oct-2-ulopyranosonic acid (Kdo) of the growing core region of lipopolysaccharide (LPS). The catalytic efficiency of HepI with the fully deacylated analogue of Escherichia coli HepI LipidA is 12-fold greater than with the fully acylated substrate, with a k(cat)/K(m) of 2.7 x 10(6) M(-1) s(-1), compared to a value of 2.2 X 10(5) M(-1) s(-1) for the Kdo(2)-LipidA substrate. Not only is this is the first demonstration that an LPS biosynthetic enzyme is catalytically enhanced by the absence of lipids, this result has significant implications for downstream enzymes that are now thought to utilize deacylated substrates.

  DOI：

  10.1021/bi201581b
• 作为产物：
  描述：

  ADP-D-glycero-beta-D-manno-heptose(2-) 生成 ADP-L-glycero-D-manno-heptose
  参考文献：
  名称：

  A Two-Base Mechanism for Escherichia coli ADP-l-glycero-d-manno-Heptose 6-Epimerase

  摘要：

  ADP-L-glycero-D-manno-heptose 6-epimerase (HldD or AGME, formerly RfaD) catalyzes the inversion of configuration at C-6' ' of the heptose moiety of ADP-D-glycero-D-manno-heptose and ADP-L-glycero-D-manno-heptose. The epimerase HldD operates in the biosynthetic pathway of L-glycero-D-manno-heptose, which is a conserved sugar in the core region of lipopolysaccharide (LPS) of Gram-negative bacteria. Previous studies support a mechanism in which HldD uses its tightly bound NADP(+) cofactor to oxidize directly at C-6' ', generating a ketone intermediate. A reduction of the ketone from the opposite face then occurs, generating the epimeric product. How the epimerase is able access both faces of the ketone intermediate with correct alignment of the three required components, NADPH, the ketone carbonyl, and a catalytic acid/base residue, is addressed here. It is proposed that the epimerase active site contains two catalytic pockets, each of which bears a catalytic acid/base residue that facilitates reduction of the C-6' ' ketone but leads to a distinct epimeric product. The ketone carbonyl may access either pocket via rotation about the C-5' '-C-6' ' bond of the sugar nucleotide and in doing so presents opposing faces to the bound cofactor. Evidence in support of the two-base mechanism is found in studies of two single mutants of the Escherichia coli K-12 epimerase, Y140F and K178M, both of which have severely compromised epimerase activities that are more than 3 orders of magnitude lower than that of the wild type. The catalytic competency of these two mutants in promoting redox chemistry is demonstrated with an alternate catalytic activity that requires only one catalytic base: dismutation of a C-6' ' aldehyde substrate analogue (ADP-beta-D-manno-hexodialdose) to an acid and an alcohol (ADP-beta-D-mannuronic acid and ADP-beta-D-mannose). This study identifies the two catalytic bases as tyrosine 140 and lysine 178. A one-step enzymatic conversion of mannose into ADP-beta-mannose is also described and used to make C-6' '-substituted derivatives of this sugar nucleotide.

  DOI：

  10.1021/bi602641m

文献信息

• Role of Escherichia coli K-12 rfa genes and the rfp gene of Shigella dysenteriae 1 in generation of lipopolysaccharide core heterogeneity and attachment of O antigen
  作者：J D Klena、R S Ashford、C A Schnaitman

  DOI：10.1128/jb.174.22.7297-7307.1992

  日期：1992.11

  The rfp gene of Shigella dysenteriae 1 and the rfa genes of Escherichia coli K-12 and Salmonella typhimurium LT2 have been studied to determine their relationship to lipopolysaccharide (LPS) core heterogeneity and their role in the attachment of O antigen to LPS. It has been inferred from the nucleotide sequence that the rfp gene encodes a protein of 41,864 Da which has a structure similar to that of RfaG protein. Expression of this gene in E. coli K-12 results in the loss of one of the three bands seen in gel analysis of the LPS and in the appearance of a new, more slowly migrating band. This is consistent with the hypothesis that Rfp is a sugar transferase which modifies a subset of core molecules so that they become substrates for attachment of S. dysenteriae O antigen. A shift in gel migration of the bands carrying S. dysenteriae O antigen and disappearance of the Rfp-modified band in strains producing O antigen suggest that the core may be trimmed or modified further before attachment of O antigen. Mutation of rfaL results in a loss of the rough LPS band which appears to be modified by Rfp and prevents the appearance of the Rfp-modified band. Thus, RfaL protein is involved in core modification and is more than just a component of the O-antigen ligase. The products of rfaK and rfaQ also appear to be involved in modification of the core prior to attachment of O antigen, and the sites of rfaK modification are different in E. coli K-12 and S. typhimurium. In contrast, mutations in rfaS and rfaZ result in changes in the LPS core but do not affect the attachment of O antigen. We propose that these genes are involved in an alternative pathway for the synthesis of rough LPS species which are similar to lipooligosaccharides of other species and which are not substrates for O-antigen attachment. All of these studies indicate that the apparent heterogeneity of E. coli K-12 LPS observed on gels is not an artifact but instead a reflection of functional differences among LPS species.

  研究了志贺菌1型的rfp基因以及大肠杆菌K-12和鼠伤寒沙门氏菌LT2的rfa基因，以确定它们与脂多糖（LPS）核心异质性的关系以及它们在O抗原与LPS结合中的作用。从核苷酸序列推断，rfp基因编码一个重量为41,864 Da的蛋白质，其结构类似于RfaG蛋白质。在大肠杆菌K-12中表达该基因会导致LPS凝胶分析中三个带中的一个消失，并出现一个新的、迁移速度更慢的带。这与Rfp是一种糖转移酶的假设一致，该酶修饰一部分核心分子，使它们成为S. dysenteriae O抗原的底物。携带S. dysenteriae O抗原的带的凝胶迁移发生变化，以及产生O抗原的菌株中Rfp修饰带的消失，暗示在O抗原结合之前，核心可能会被修剪或进一步修饰。rfaL基因突变导致粗糙的LPS带消失，该带似乎被Rfp修饰，并防止Rfp修饰带的出现。因此，RfaL蛋白参与核心修饰，不仅是O抗原连接酶的组成部分。rfaK和rfaQ的产物似乎也参与了O抗原结合之前的核心修饰，而在大肠杆菌K-12和鼠伤寒沙门氏菌中，rfaK修饰的位点不同。相反，rfaS和rfaZ的突变导致LPS核心的变化，但不影响O抗原的连接。我们提出这些基因参与了合成类似于其他物种的脂寡糖的粗糙LPS物种的替代途径，这些物种不是O抗原连接的底物。所有这些研究表明，大肠杆菌K-12 LPS在凝胶上观察到的明显异质性不是人为的，而是不同LPS物种之间功能差异的反映。
• Lipopolysaccharide Biosynthesis without the Lipids: Recognition Promiscuity of<i>Escherichia coli</i>Heptosyltransferase I
  作者：Daniel J. Czyzyk、Cassie Liu、Erika A. Taylor

  DOI：10.1021/bi201581b

  日期：2011.12.13

  Heptosyltransferase I (HepI) is responsible for the transfer of L-glycero-D-manno-heptose to a 3-deoxy-alpha-D-oct-2-ulopyranosonic acid (Kdo) of the growing core region of lipopolysaccharide (LPS). The catalytic efficiency of HepI with the fully deacylated analogue of Escherichia coli HepI LipidA is 12-fold greater than with the fully acylated substrate, with a k(cat)/K(m) of 2.7 x 10(6) M(-1) s(-1), compared to a value of 2.2 X 10(5) M(-1) s(-1) for the Kdo(2)-LipidA substrate. Not only is this is the first demonstration that an LPS biosynthetic enzyme is catalytically enhanced by the absence of lipids, this result has significant implications for downstream enzymes that are now thought to utilize deacylated substrates.
• A Two-Base Mechanism for <i>Escherichia coli</i> ADP-<scp>l</scp>-<i>glycero</i>-<scp>d</scp>-<i>manno</i>-Heptose 6-Epimerase
  作者：James P. Morrison、Martin E. Tanner

  DOI：10.1021/bi602641m

  日期：2007.3.1

  ADP-L-glycero-D-manno-heptose 6-epimerase (HldD or AGME, formerly RfaD) catalyzes the inversion of configuration at C-6' ' of the heptose moiety of ADP-D-glycero-D-manno-heptose and ADP-L-glycero-D-manno-heptose. The epimerase HldD operates in the biosynthetic pathway of L-glycero-D-manno-heptose, which is a conserved sugar in the core region of lipopolysaccharide (LPS) of Gram-negative bacteria. Previous studies support a mechanism in which HldD uses its tightly bound NADP(+) cofactor to oxidize directly at C-6' ', generating a ketone intermediate. A reduction of the ketone from the opposite face then occurs, generating the epimeric product. How the epimerase is able access both faces of the ketone intermediate with correct alignment of the three required components, NADPH, the ketone carbonyl, and a catalytic acid/base residue, is addressed here. It is proposed that the epimerase active site contains two catalytic pockets, each of which bears a catalytic acid/base residue that facilitates reduction of the C-6' ' ketone but leads to a distinct epimeric product. The ketone carbonyl may access either pocket via rotation about the C-5' '-C-6' ' bond of the sugar nucleotide and in doing so presents opposing faces to the bound cofactor. Evidence in support of the two-base mechanism is found in studies of two single mutants of the Escherichia coli K-12 epimerase, Y140F and K178M, both of which have severely compromised epimerase activities that are more than 3 orders of magnitude lower than that of the wild type. The catalytic competency of these two mutants in promoting redox chemistry is demonstrated with an alternate catalytic activity that requires only one catalytic base: dismutation of a C-6' ' aldehyde substrate analogue (ADP-beta-D-manno-hexodialdose) to an acid and an alcohol (ADP-beta-D-mannuronic acid and ADP-beta-D-mannose). This study identifies the two catalytic bases as tyrosine 140 and lysine 178. A one-step enzymatic conversion of mannose into ADP-beta-mannose is also described and used to make C-6' '-substituted derivatives of this sugar nucleotide.