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Knirel Y, Bailey M. Nikolay Konstantinovich Kochetkov 1915–2005. Adv Carbohydr Chem Biochem 2007; 61:2-28. [DOI: 10.1016/s0065-2318(07)61001-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Petrová P, Monteiro C, Hervé du Penhoat C, Koca J, Imberty A. Conformational behavior of nucleotide-sugar in solution: molecular dynamics and NMR study of solvated uridine diphosphate-glucose in the presence of monovalent cations. Biopolymers 2001; 58:617-35. [PMID: 11285558 DOI: 10.1002/1097-0282(200106)58:7<617::aid-bip1035>3.0.co;2-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nucleotide-sugars are metabolites of primary importance in the biosynthesis of polysaccharides and glycoconjugates since they serve as sugar donors in the reactions of glycosyltransferases, enzymes that displays a high specificity for both donors and acceptors. In order to determine the conformational behavior of uridinediphosphoglucose in dilute aqueous solution that includes a physiologically relevant concentration of salt, parallel NMR and molecular modeling investigations have been conducted. Nine molecular dynamics trajectories of 3 ns each were calculated in presence of explicit water and monovalent cations with the use of the AMBER force field with recently developed energy parameters for nucleotide-sugars (P. Petrova, J. Koca, and A. Imberty, Journal of American Chemical Society, 1999, vol. 121, pp. 5535-5547). Theoretical nuclear Overhauser effect data were calculated from these simulations using a model-free approach that takes into account internal motions. Comparison of theoretical and experimental data gives excellent agreement for the region surrounding the glucose-phosphate linkage including the pyrophosphate linkage itself. Less satisfactory agreement is obtained for the ribose ring and the base orientations. On the whole, both NMR and molecular dynamics simulations predict the molecule to be flexible, and to visit a large number of conformations while maintaining an extended overall shape.
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Affiliation(s)
- P Petrová
- CERMAV-CNRS, BP 53, F-38041 Grenoble Cedex 9, France
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Monteiro C, Neyret S, Leforestier J, Hervé du Penhoat C. Solution conformation of various uridine diphosphoglucose salts as probed by NMR spectroscopy. Carbohydr Res 2000; 329:141-55. [PMID: 11086694 DOI: 10.1016/s0008-6215(00)00166-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The solution conformations of uridine diphosphoglucose (UDP-Glc) under a variety of conditions (solvent, ionic strength, various mono- and divalent cations) have been studied by NMR spectroscopy (1H, 13C, 31P, and 25Mg). In the case of divalent cations (Ca2+, Mg2+, Mn2+) the phosphate oxygens are the preferred coordination sites and analysis of the 25Mg linewidths of solutions with various [Mg2+]/[UDP-Glc] ratios, indicates that the 1:1 Mg2+ UDP-Glc complex is the major species. From 13C relaxation data and hydrodynamic theory, it has been demonstrated that under all conditions UDP-Glc adopts a fairly extended overall shape and that magnesium ions lead to a significant increase in the average length of the UDP-Glc molecule as compared to monovalent cations. Thus, one of the roles of the metal ion in enzymic reactions involving nucleotide sugars may be to preorganize the nucleotide sugar.
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Affiliation(s)
- C Monteiro
- Centre de Recherches sur les Macromolécules Végétales, CNRS (associated with University Joseph Fourier), Grenoble, France
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Liger D, Masson A, Blanot D, van Heijenoort J, Parquet C. Over-production, purification and properties of the uridine-diphosphate-N-acetylmuramate:L-alanine ligase from Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 230:80-7. [PMID: 7601127 DOI: 10.1111/j.1432-1033.1995.0080i.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The UDP-N-acetylmuramate:L-alanine ligase of Escherichia coli was over-produced in strains harbouring recombinant plasmids bearing the murC gene under the control of the lac or trc promoter. Plasmid pAM1005, in which the promoter and ribosome-binding site region of murC were removed and in which the gene was directly under the control of promoter trc, led to a 2000-fold amplification of the L-alanine-adding activity after induction by isopropyl-thio-beta-D-galactopyranoside. The murC gene product was visualized as a 50-kDa protein accounting for approximately 50% of the cell protein. A two-step purification led to 1 g of a homogeneous protein from an 18-1 culture. The N-terminal sequence of the purified protein correlated with the nucleotide sequence of the murC gene. The presence of 2-mercaptoethanol and glycerol was essential for the stability of the enzyme. The Km values for UDP-N-acetylmuramic acid, L-alanine and ATP/Mg2+ were estimated at 100, 20 and 450 microM, respectively. Under the optimal in vitro conditions a turnover number of 928 min-1 was calculated and a copy number/cell of 600 could be roughly estimated. The specificity of the enzyme for its substrates was investigated with various analogues. The enzyme also catalysed the reverse reaction.
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Affiliation(s)
- D Liger
- Unité de Recherche Associée 1131 du Centre National de la Recherche Scientifique, Université Paris-Sud, France
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Control of glycoprotein synthesis. Purification of UDP-N-acetylglucosamine:alpha-D-mannoside beta 1-2 N-acetylglucosaminyltransferase II from rat liver. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)45642-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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7
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Abo-Ghalia M, Michaud C, Blanot D, van Heijenoort J. Specificity of the uridine-diphosphate-N-acetylmuramyl-L-alanyl-D-glutamate: meso-2,6-diaminopimelate synthetase from Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 153:81-7. [PMID: 3905407 DOI: 10.1111/j.1432-1033.1985.tb09269.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To investigate the specificity of the uridine-diphosphate-N-acetylmuramyl-L-alanyl-D-glutamate: meso-2,6-diaminopimelate synthetase, various compounds mimicking more or less different parts of the UDP-MurNAc-L-Ala-D-Glu substrate were prepared. Their size ranged from that of uridine or L-Ala-D-Glu to that of the whole nucleotide substrate. Chemical synthesis led to N alpha-acyl-dipeptides, in which the acyl group mimicked the MurNAc moiety, and to glycopeptides MurNAc(alpha or beta-Me)-L-Ala-D-Glu, in which the anomeric function is blocked. Partial degradation or chemical modification of the substrate UDP-MurNAc-L-Ala-D-Glu afforded: MurOHNAc-L-Ala-D-Glu, P1-MurNAc-L-Ala-D-Glu, and DDP-MurNAc-L-Ala-D-Glu (DDP = dihydrouridine-diphosphate). All these compounds were tested as substrates or (and) inhibitors of the reaction catalyzed by the A2pm-adding enzyme, which, after partial purification, was obtained in two active forms. Among the compounds tested as substrates, only DDP-MurNAc-L-Ala-D-Glu was a good one. The Km for this compound was 97 microM versus 55 microM for the natural substrate. Among the various compounds tested as inhibitors, only P1-MurNAc-L-Ala-D-Glu and MurNAc(alpha or beta-Me)-L-Ala-D-Glu had a significant inhibitory effect at 1mM. Apparently, no particular portion of the molecule is predominantly responsible for its recognition by the enzyme. In other words, multiple sites located over the whole molecule are required for a proper recognition and determine the high specificity of this activity. Therefore, to obtain efficient competitive inhibitors it is necessary to synthesize molecules very similar in size and structure to the natural substrate.
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Zemek J, Kucár S, Zámocký J. Transglycosylic reactions of deoxysugars. Biosynthesis of deoxy analogues of starch. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 89:291-5. [PMID: 308877 DOI: 10.1111/j.1432-1033.1978.tb20926.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biosynthesis of starch was investigated in the reaction catalyzed by plant alpha(1 leads to 4)-glucan phosphorylase using alpha-D-glucopyranosyl phosphate and its deoxy analogues as substrates. It was found that the hydroxyl groups at the positions C-2, C-3, C-4 and C-6 in the glucose moiety of the molecule of alpha-D-glucopyranosyl phosphate are not essential for its substrate properties in the transglycosylic reaction. The affinity of plant (alpha(1 leads to 4)-glucan phosphorylase and the rate of hexose incorporation into alpha(1 leads to 4)-glucan decreases in the following sequence: alpha-D-glucopyranosyl phos-phosphate, 2-deoxy-, 6-deoxy, 4-deoxy, and 3-deoxy-alpha-D-glucopyranosyl phosphate. The deoxyglucosyl analogues of alpha-D-glucosylpyranosyl phosphate act as competitive inhibitors on the elongation reaction of the alpha(1 leads to 4) chains of starch. It was found that more than one residue of 2-deoxy-D-glucose or 6-deoxy-D-glucose can be incorporated into the nonreducing terminus of alpha(1 leads to 4)-glucan chains of starch.
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Graham TL, Whistler RL. Enzymatic synthesis and reactions of uridine 5'-(5-thio-alphaD-glucopyranosyl pyrophosphate). Arch Biochem Biophys 1975; 171:721-6. [PMID: 970 DOI: 10.1016/0003-9861(75)90084-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Druzhinina TN, Kusov YY, Shibaev VN, Kochetkov NK. Interaction of uridine diphosphate glucose with calf liver uridine diphosphate glucose dehydrogenase. Significance of hydroxyl groups at C-3, C-4 and C-6 of hexosyl residue. BIOCHIMICA ET BIOPHYSICA ACTA 1975; 403:1-8. [PMID: 1174541 DOI: 10.1016/0005-2744(75)90002-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analogs of uridine diphosphate glucose (UDPGlc) with a modified hexosyl residue which contained a deoxy-unit at C-3 or C-4 were tested as substrates of calf liver UDPGlc dehydrogenase (EC 1.1.1.22). The 3-deoxyglucose derivative was found not to serve as a substrate for the enzyme whereas the 4-deoxyglucose analog was able to participate in the reaction. The apparent Km of the latter was 5.3 times that of UDPGlc and the relative V was 0.04. The reaction product was identified as uridine diphosphate deoxyhexuronic acid. UDP-deoxyhexoses were non-competitive inhibitors of UDPGlc enzymic oxidation, inhibition increased in the sequence: 2-deoxy-less than 3-and 6-deoxy-less than 4-deoxyglucose derivative. The significance of different HO-groups in hexosyl residue for interaction of UDPGlc with the enzyme is discussed.
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Kang UG, Nolan LD, Frey PA. Uridine diphosphate galactose-4-epimerase. Uridine monophosphate-dependent reduction by alpha- and beta-D-glucose. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)40914-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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12
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Effect of glucose analogues on synthesis of sugar nucleotides and oligosaccharides inSaccharomyces cerevisiae. Appl Microbiol Biotechnol 1975. [DOI: 10.1007/bf01880619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Analogs of glucose uridine diphosphate: Synthesis and reaction with enzymes. Russ Chem Bull 1974. [DOI: 10.1007/bf00927283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Zemek J, Kucár S, Bauer S. Transglycosylic reactions of nucleotides of deoxy-sugars. 3-Deoxy-D-glucose, 4-deoxy-D-glucose and 6-deoxy-D-glucose incorporation into glycogen. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 40:195-9. [PMID: 4589548 DOI: 10.1111/j.1432-1033.1973.tb03185.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Analogs of carbohydrate metabolism coenzymes Communication 17. Some C-5 substituted heterocyclic analogs of uridine diphosphate glucose. Russ Chem Bull 1973. [DOI: 10.1007/bf00929401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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17
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Some problems in the chemistry and biochemistry of carbohydrates. Russ Chem Bull 1972. [DOI: 10.1007/bf00851188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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18
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Larsen B, Haug A. Biosynthesis of alginate. 3. Tritium incorporation with polymannuronic acid 5-epimerase from Azotobacter vinelandii. Carbohydr Res 1971; 20:225-32. [PMID: 4339944 DOI: 10.1016/s0008-6215(00)81375-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Cohn R, Segal S. Regulation of mammalian liver uridine diphosphogalactose 4-epimerase by pyrimidine nucleotides. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 222:533-6. [PMID: 5491232 DOI: 10.1016/0304-4165(70)90148-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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21
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Gabrieljan ND, Lapina EB, Spiridonova SM, Shibaev VN, Budowsky EI, Kochetkov NK. The interaction of adenosine diphosphate glucose and its synthetic analogs with uridine diphosphate glucose-fructose glucosyltransferase from pea seedlings. BIOCHIMICA ET BIOPHYSICA ACTA 1969; 185:478-81. [PMID: 5808709 DOI: 10.1016/0005-2744(69)90445-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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22
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Kochetkov N, Budowsky E, Druzhinina T, Gabrieljan N, Komlev I, Kusov Y, Shibaev V. The synthesis of uridine 5′-(3-deoxy-α-d-ribo-hexopyranosyl and -4-deoxy-α-d-yxlo-hexopyranosyl disodium pyrophosphates), and their behaviour in some enzymic reactions. Carbohydr Res 1969. [DOI: 10.1016/s0008-6215(00)81097-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Kochetkov NK, Budovskii �I, Shibaev VN, Kusov YY. Analogs of coenzymes of carbohydrate metabolism. Russ Chem Bull 1969. [DOI: 10.1007/bf00922867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Cohn R, Segal S. Some characteristics and developmental aspects of rat uridine diphosphogalactose 4-epimerase. BIOCHIMICA ET BIOPHYSICA ACTA 1969; 171:333-41. [PMID: 4304332 DOI: 10.1016/0005-2744(69)90166-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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26
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Farkas V, Biely P, Bauer S. Transglycosylic reactions of nucleotides of 2-deoxy-sugars. I. Biosynthesis of 2-deoxysucrose. BIOCHIMICA ET BIOPHYSICA ACTA 1968; 165:63-7. [PMID: 5672845 DOI: 10.1016/0304-4165(68)90188-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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Kinetics of the acid hydrolysis of uridine diphosphate glucose and 3-N-methyluridine diphosphate glucose. Chem Nat Compd 1968. [DOI: 10.1007/bf00571136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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28
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Analogs of coenzymes of carbohydrate metabolism. Chem Nat Compd 1968. [DOI: 10.1007/bf00568023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Salo WL, Nordin JH, Peterson DR, Bevill RD, Kirkwood S. The specificity of UDP-glucose 4-epimerase from the yeast Saccharomyces fragilis. BIOCHIMICA ET BIOPHYSICA ACTA 1968; 151:484-92. [PMID: 5636379 DOI: 10.1016/0005-2744(68)90116-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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30
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The synthesis of uridine 5-(6-deoxy-α-d-glucopyranosyl dihydrogen pyrophosphate) and its interaction with UDP-glucose dehydrogenase. Carbohydr Res 1967. [DOI: 10.1016/s0008-6215(00)80518-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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