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Volumn 51, Issue 44, 2012, Pages 8844-8855

Human UDP-α- d -xylose synthase and escherichia coli ArnA conserve a conformational shunt that controls whether xylose or 4-keto-xylose is produced

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; COFACTORS; CONFORMATIONAL CHANGE; D-GLUCURONIC ACID; D-XYLOSE; DECARBOXYLASES; RATE EQUATIONS; SIDE PRODUCTS; SLOW RELEASE; STIMULATORY EFFECTS; STRUCTURAL ELEMENTS; SYNTHASES;

EID: 84868574639     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi301135b     Document Type: Article
Times cited : (19)

References (52)
  • 1
    • 0035997376 scopus 로고    scopus 로고
    • Order out of chaos: Assembly of ligand binding sites in heparan sulfate
    • Esko, J. D. and Selleck, S. B. (2002) Order out of chaos: assembly of ligand binding sites in heparan sulfate Annu. Rev. Biochem. 71, 435-471
    • (2002) Annu. Rev. Biochem. , vol.71 , pp. 435-471
    • Esko, J.D.1    Selleck, S.B.2
  • 2
    • 21744431575 scopus 로고    scopus 로고
    • The sweet and sour of cancer: Glycans as novel therapeutic targets
    • Fuster, M. M. and Esko, J. D. (2005) The sweet and sour of cancer: glycans as novel therapeutic targets Nat. Rev. Cancer 5, 526-542
    • (2005) Nat. Rev. Cancer , vol.5 , pp. 526-542
    • Fuster, M.M.1    Esko, J.D.2
  • 4
    • 0024297813 scopus 로고
    • Tumor formation dependent on proteoglycan biosynthesis
    • Esko, J. D., Rostand, K. S., and Weinke, J. L. (1988) Tumor formation dependent on proteoglycan biosynthesis Science 241, 1092-1096
    • (1988) Science , vol.241 , pp. 1092-1096
    • Esko, J.D.1    Rostand, K.S.2    Weinke, J.L.3
  • 6
    • 0035930615 scopus 로고    scopus 로고
    • Biosynthesis of the linkage region of glycosaminoglycans: Cloning and activity of galactosyltransferase II, the sixth member of the beta 1,3-galactosyltransferase family (beta 3GalT6)
    • Bai, X., Zhou, D., Brown, J. R., Crawford, B. E., Hennet, T., and Esko, J. D. (2001) Biosynthesis of the linkage region of glycosaminoglycans: cloning and activity of galactosyltransferase II, the sixth member of the beta 1,3-galactosyltransferase family (beta 3GalT6) J. Biol. Chem. 276, 48189-48195
    • (2001) J. Biol. Chem. , vol.276 , pp. 48189-48195
    • Bai, X.1    Zhou, D.2    Brown, J.R.3    Crawford, B.E.4    Hennet, T.5    Esko, J.D.6
  • 7
    • 0036818369 scopus 로고    scopus 로고
    • Biosynthesis of chondroitin/dermatan sulfate
    • Silbert, J. E. and Sugumaran, G. (2002) Biosynthesis of chondroitin/dermatan sulfate IUBMB Life 54, 177-186
    • (2002) IUBMB Life , vol.54 , pp. 177-186
    • Silbert, J.E.1    Sugumaran, G.2
  • 8
    • 0036818793 scopus 로고    scopus 로고
    • Heparin and heparan sulfate biosynthesis
    • Sugahara, K. and Kitagawa, H. (2002) Heparin and heparan sulfate biosynthesis IUBMB Life 54, 163-175
    • (2002) IUBMB Life , vol.54 , pp. 163-175
    • Sugahara, K.1    Kitagawa, H.2
  • 9
    • 34250878429 scopus 로고    scopus 로고
    • Notch signaling in normal and disease states: Possible therapies related to glycosylation
    • Rampal, R., Luther, K. B., and Haltiwanger, R. S. (2007) Notch signaling in normal and disease states: possible therapies related to glycosylation Curr. Mol. Med. 7, 427-445
    • (2007) Curr. Mol. Med. , vol.7 , pp. 427-445
    • Rampal, R.1    Luther, K.B.2    Haltiwanger, R.S.3
  • 12
    • 84855515852 scopus 로고    scopus 로고
    • Dystroglycan function requires xylosyl- and glucuronyltransferase activities of LARGE
    • Inamori, K., Yoshida-Moriguchi, T., Hara, Y., Anderson, M. E., Yu, L., and Campbell, K. P. (2012) Dystroglycan function requires xylosyl- and glucuronyltransferase activities of LARGE Science 335, 93-96
    • (2012) Science , vol.335 , pp. 93-96
    • Inamori, K.1    Yoshida-Moriguchi, T.2    Hara, Y.3    Anderson, M.E.4    Yu, L.5    Campbell, K.P.6
  • 15
    • 84866118842 scopus 로고    scopus 로고
    • Structure and mechanism of human UDP-xylose synthase: Evidence for a promoting role of sugar ring distortion in a three-step catalytic conversion of UDP-glucuronic acid
    • Eixelsberger, T., Sykora, S., Egger, S., Brunsteiner, M., Kavanagh, K. L., Oppermann, U., Brecker, L., and Nidetzky, B. (2012) Structure and mechanism of human UDP-xylose synthase: evidence for a promoting role of sugar ring distortion in a three-step catalytic conversion of UDP-glucuronic acid J. Biol. Chem. 287, 31349-31358
    • (2012) J. Biol. Chem. , vol.287 , pp. 31349-31358
    • Eixelsberger, T.1    Sykora, S.2    Egger, S.3    Brunsteiner, M.4    Kavanagh, K.L.5    Oppermann, U.6    Brecker, L.7    Nidetzky, B.8
  • 17
    • 0017669210 scopus 로고
    • UDP-glucuronate carboxy-lyase in cultured chondrocytes
    • John, K. V., Schwartz, N. B., and Ankel, H. (1977) UDP-glucuronate carboxy-lyase in cultured chondrocytes J. Biol. Chem. 252, 6707-6710
    • (1977) J. Biol. Chem. , vol.252 , pp. 6707-6710
    • John, K.V.1    Schwartz, N.B.2    Ankel, H.3
  • 18
    • 0035834048 scopus 로고    scopus 로고
    • Functional cloning and characterization of a UDP- glucuronic acid decarboxylase: The pathogenic fungus Cryptococcus neoformans elucidates UDP-xylose synthesis
    • Bar-Peled, M., Griffith, C. L., and Doering, T. L. (2001) Functional cloning and characterization of a UDP- glucuronic acid decarboxylase: the pathogenic fungus Cryptococcus neoformans elucidates UDP-xylose synthesis Proc. Natl. Acad. Sci. U. S. A. 98, 12003-12008
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 12003-12008
    • Bar-Peled, M.1    Griffith, C.L.2    Doering, T.L.3
  • 19
    • 0036918914 scopus 로고    scopus 로고
    • Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms
    • Harper, A. D. and Bar-Peled, M. (2002) Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms Plant Physiol. 130, 2188-2198
    • (2002) Plant Physiol. , vol.130 , pp. 2188-2198
    • Harper, A.D.1    Bar-Peled, M.2
  • 20
    • 0036857412 scopus 로고    scopus 로고
    • Purification and cDNA cloning of UDP-D-glucuronate carboxy-lyase (UDP- d -xylose synthase) from pea seedlings
    • Kobayashi, M., Nakagawa, H., Suda, I., Miyagawa, I., and Matoh, T. (2002) Purification and cDNA cloning of UDP-D-glucuronate carboxy-lyase (UDP- d -xylose synthase) from pea seedlings Plant Cell Physiol. 43, 1259-1265
    • (2002) Plant Cell Physiol. , vol.43 , pp. 1259-1265
    • Kobayashi, M.1    Nakagawa, H.2    Suda, I.3    Miyagawa, I.4    Matoh, T.5
  • 21
    • 20444377995 scopus 로고    scopus 로고
    • Biosynthesis of UDP-xylose: Characterization of membrane-bound AtUxs2
    • Pattathil, S., Harper, A. D., and Bar-Peled, M. (2005) Biosynthesis of UDP-xylose: characterization of membrane-bound AtUxs2 Planta 221, 538-548
    • (2005) Planta , vol.221 , pp. 538-548
    • Pattathil, S.1    Harper, A.D.2    Bar-Peled, M.3
  • 22
    • 6344289277 scopus 로고    scopus 로고
    • Crystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. A key enzyme for lipid A modification with 4-amino-4-deoxy- l -arabinose and polymyxin resistance
    • Gatzeva-Topalova, P. Z., May, A. P., and Sousa, M. C. (2004) Crystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. A key enzyme for lipid A modification with 4-amino-4-deoxy- l -arabinose and polymyxin resistance Biochemistry 43, 13370-13379
    • (2004) Biochemistry , vol.43 , pp. 13370-13379
    • Gatzeva-Topalova, P.Z.1    May, A.P.2    Sousa, M.C.3
  • 23
    • 0037169485 scopus 로고    scopus 로고
    • Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy- l -arabinose
    • Breazeale, S. D., Ribeiro, A. A., and Raetz, C. R. (2002) Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy- l -arabinose J. Biol. Chem. 277, 2886-2896
    • (2002) J. Biol. Chem. , vol.277 , pp. 2886-2896
    • Breazeale, S.D.1    Ribeiro, A.A.2    Raetz, C.R.3
  • 24
    • 0016619523 scopus 로고
    • Molar Absorptivities of β-NADH and β-NAD at 260 nm
    • Hald, E., Lehmann, P., and Ziegenhorn, J. (1975) Molar Absorptivities of β-NADH and β-NAD at 260 nm Clin. Chem. 21, 884-887
    • (1975) Clin. Chem. , vol.21 , pp. 884-887
    • Hald, E.1    Lehmann, P.2    Ziegenhorn, J.3
  • 26
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski, Z. and Minor, W. (1996) Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276, 307-326
    • (1996) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 29
    • 0030767713 scopus 로고    scopus 로고
    • Free R Value: Cross-validation in Crystallography
    • Brunger, A. T. (1997) Free R Value: Cross-validation in Crystallography Methods Enzymol. 277B, 366-396
    • (1997) Methods Enzymol. , vol.277 , pp. 366-396
    • Brunger, A.T.1
  • 30
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project, N
    • Collaborative Computational Project, N (1994) The CCP4 suite: programs for protein crystallography Acta Crystallogr., Sect. D 50, 760-763
    • (1994) Acta Crystallogr., Sect. D , vol.50 , pp. 760-763
  • 31
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics Acta Crystallogr., Sect. D 60, 2126-2132
    • (2004) Acta Crystallogr., Sect. D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 32
    • 20744455042 scopus 로고    scopus 로고
    • Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy- l -arabinose biosynthesis
    • Williams, G. J., Breazeale, S. D., Raetz, C. R., and Naismith, J. H. (2005) Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy- l -arabinose biosynthesis J. Biol. Chem. 280, 23000-23008
    • (2005) J. Biol. Chem. , vol.280 , pp. 23000-23008
    • Williams, G.J.1    Breazeale, S.D.2    Raetz, C.R.3    Naismith, J.H.4
  • 33
    • 20444377731 scopus 로고    scopus 로고
    • Structure and mechanism of ArnA: Conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance
    • Gatzeva-Topalova, P. Z., May, A. P., and Sousa, M. C. (2005) Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance Structure 13, 929-942
    • (2005) Structure , vol.13 , pp. 929-942
    • Gatzeva-Topalova, P.Z.1    May, A.P.2    Sousa, M.C.3
  • 35
    • 0033824470 scopus 로고    scopus 로고
    • DaliLite workbench for protein structure comparison
    • Holm, L. and Park, J. (2000) DaliLite workbench for protein structure comparison Bioinformatics 16, 566-567
    • (2000) Bioinformatics , vol.16 , pp. 566-567
    • Holm, L.1    Park, J.2
  • 36
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace, A. C., Laskowski, R. A., and Thornton, J. M. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Eng. 8, 127-134
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 37
    • 0023927904 scopus 로고
    • Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure
    • Richards, F. M. and Kundrot, C. E. (1988) Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure Proteins 3, 71-84
    • (1988) Proteins , vol.3 , pp. 71-84
    • Richards, F.M.1    Kundrot, C.E.2
  • 38
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
    • Hayward, S. and Berendsen, H. J. (1998) Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme Proteins 30, 144-154
    • (1998) Proteins , vol.30 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.2
  • 39
    • 0014940726 scopus 로고
    • Kinetic aspects of regulation of metabolic processes. The hysteretic enzyme concept
    • Frieden, C. (1970) Kinetic aspects of regulation of metabolic processes. The hysteretic enzyme concept. J. Biol. Chem. 245, 5788-5799
    • (1970) J. Biol. Chem. , vol.245 , pp. 5788-5799
    • Frieden, C.1
  • 40
    • 0029150760 scopus 로고
    • Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
    • Zhang, X. J., Wozniak, J. A., and Matthews, B. W. (1995) Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme J. Mol. Biol. 250, 527-552
    • (1995) J. Mol. Biol. , vol.250 , pp. 527-552
    • Zhang, X.J.1    Wozniak, J.A.2    Matthews, B.W.3
  • 42
    • 0028908071 scopus 로고
    • Transition structures of hydride transfer reactions of protonated pyridinium ion with 1,4-dihydropyridine and protonated nicotinamide with 1,4-dihydronicotinamide
    • Wu, Y., Lai, D. K. W., and Houk, K. N. (1995) Transition structures of hydride transfer reactions of protonated pyridinium ion with 1,4-dihydropyridine and protonated nicotinamide with 1,4-dihydronicotinamide J. Am. Chem. Soc. 117, 4100-4108
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 4100-4108
    • Wu, Y.1    Lai, D.K.W.2    Houk, K.N.3
  • 43
    • 0030879888 scopus 로고    scopus 로고
    • Orbital steering in the catalytic power of enzymes: Small structural changes with large catalytic consequences
    • Mesecar, A. D., Stoddard, B. L., and Koshland, D. E., Jr. (1997) Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences Science 277, 202-206
    • (1997) Science , vol.277 , pp. 202-206
    • Mesecar, A.D.1    Stoddard, B.L.2    Koshland Jr., D.E.3
  • 44
    • 0034161331 scopus 로고    scopus 로고
    • Flavoenzymes: Diverse catalysts with recurrent features
    • Fraaije, M. W. and Mattevi, A. (2000) Flavoenzymes: diverse catalysts with recurrent features Trends Biochem. Sci. 25, 126-132
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 126-132
    • Fraaije, M.W.1    Mattevi, A.2
  • 46
    • 0028038824 scopus 로고
    • Refined structure of concanavalin A complexed with methyl alpha-D-mannopyranoside at 2.0 Å resolution and comparison with the saccharide-free structure
    • Naismith, J. H., Emmerich, C., Habash, J., Harrop, S. J., Helliwell, J. R., Hunter, W. N., Raftery, J., Kalb, A. J., and Yariv, J. (1994) Refined structure of concanavalin A complexed with methyl alpha-D-mannopyranoside at 2.0 Å resolution and comparison with the saccharide-free structure Acta Crystallogr., Sect. D 50, 847-858
    • (1994) Acta Crystallogr., Sect. D , vol.50 , pp. 847-858
    • Naismith, J.H.1    Emmerich, C.2    Habash, J.3    Harrop, S.J.4    Helliwell, J.R.5    Hunter, W.N.6    Raftery, J.7    Kalb, A.J.8    Yariv, J.9
  • 47
    • 0032878247 scopus 로고    scopus 로고
    • The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A
    • Bouckaert, J., Hamelryck, T. W., Wyns, L., and Loris, R. (1999) The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1- O)Me in complex with concanavalin A J. Biol. Chem. 274, 29188-29195
    • (1999) J. Biol. Chem. , vol.274 , pp. 29188-29195
    • Bouckaert, J.1    Hamelryck, T.W.2    Wyns, L.3    Loris, R.4
  • 48
    • 58049202316 scopus 로고    scopus 로고
    • Involvement of water in carbohydrate-protein binding: Concanavalin A revisited
    • Kadirvelraj, R., Foley, B. L., Dyekjaer, J. D., and Woods, R. J. (2008) Involvement of water in carbohydrate-protein binding: concanavalin A revisited J. Am. Chem. Soc. 130, 16933-16942
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 16933-16942
    • Kadirvelraj, R.1    Foley, B.L.2    Dyekjaer, J.D.3    Woods, R.J.4
  • 49
    • 0031777148 scopus 로고    scopus 로고
    • Advantages in the analysis of UDP-sugars by capillary electrophoresis-comparison of the conventional HPLC method with two new capillary electrophoretic micro-procedures
    • Xu, G., Lehmann, R., Schleicher, E., Haring, H. U., and Liebich, H. (1998) Advantages in the analysis of UDP-sugars by capillary electrophoresis-comparison of the conventional HPLC method with two new capillary electrophoretic micro-procedures Biomed. Chromatogr. 12, 113-115
    • (1998) Biomed. Chromatogr. , vol.12 , pp. 113-115
    • Xu, G.1    Lehmann, R.2    Schleicher, E.3    Haring, H.U.4    Liebich, H.5
  • 50
    • 77950571350 scopus 로고    scopus 로고
    • Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family
    • Gu, X., Glushka, J., Yin, Y., Xu, Y., Denny, T., Smith, J., Jiang, Y., and Bar-Peled, M. (2010) Identification of a bifunctional UDP-4-keto-pentose/ UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family J. Biol. Chem. 285, 9030-9040
    • (2010) J. Biol. Chem. , vol.285 , pp. 9030-9040
    • Gu, X.1    Glushka, J.2    Yin, Y.3    Xu, Y.4    Denny, T.5    Smith, J.6    Jiang, Y.7    Bar-Peled, M.8
  • 51
    • 79960444742 scopus 로고    scopus 로고
    • Crystal structure of UDP-galactose 4-epimerase from the hyperthermophilic archaeon Pyrobaculum calidifontis
    • Sakuraba, H., Kawai, T., Yoneda, K., and Ohshima, T. (2011) Crystal structure of UDP-galactose 4-epimerase from the hyperthermophilic archaeon Pyrobaculum calidifontis Arch. Biochem. Biophys. 512, 126-134
    • (2011) Arch. Biochem. Biophys. , vol.512 , pp. 126-134
    • Sakuraba, H.1    Kawai, T.2    Yoneda, K.3    Ohshima, T.4
  • 52
    • 0030915704 scopus 로고    scopus 로고
    • Improved R-factors for diffraction data analysis in macromolecular crystallography [published erratum appears in Nat. Struct. Biol. 1997 Jul;4(7):592]
    • Diederichs, K. and Karplus, P. A. (1997) Improved R-factors for diffraction data analysis in macromolecular crystallography [published erratum appears in Nat. Struct. Biol. 1997 Jul;4(7):592] Nat. Struct. Biol. 4, 269-275
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 269-275
    • Diederichs, K.1    Karplus, P.A.2


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