GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from Escherichia coli, a key enzyme in the biosynthesis of GDP-L-fucose, displays the structural characteristics of the RED protein homology superfamily

Structure

Volumn 6, Issue 11, 1998, Pages 1453-1465

  Rizzi, Menico ^a,b   Tonetti, Michela ^c   Vigevani, Pierpaolo ^b   Sturla, Laura ^c   Bisso, Angela ^c   De Flora, Antonio ^c   Bordo, Domenico ^c   Bolognesi, Martino ^c  

^a UNIVERSITY OF EASTERN PIEDMONT   (Italy)

^b UNIVERSITY OF PAVIA   (Italy)

^c UNIVERSITY OF GENOA   (Italy)

Author keywords

Epimerase reductase structure; GDP fucose; Glycoconjugates biosynthesis; Leukocyte adhesion deficiency; NADP+ selection; Short chain dehydrogenase

Indexed keywords

EID: 0032534052     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00144-0     Document Type: Article

References (53)

1. Flowers, H.M. (1981). Chemistry and Biochemistry of D- and L-fucose. In Advances in Carbohydrate Chemistry and Biochemistry. (Stewart-Tipson, R and Norton, D, eds), 39 pp. 279-345, Academic Press, UK.
2. Varki, A. (1994). Selectin ligands. Proc. Natl Acad. Sci. USA 91, 7390-7397.
3. Etzioni, A., et al., & Gershoni-Baruch, R. (1992). Brief report: recurrent severe infections caused by a novel leukocyte adhesion deficiency. N. Engl. J. Med. 327, 1789-1792.
4. McEver, R.P. (1997). Selectin-carbohydrate interactions during inflammation and metastasis. Glycoconj. J. 14, 585-591.
5. Abeijon, C., Mandon, E.C. & Hirschberg, C.B. (1997). Transporters of nucleotide-sugars, nucleotide sulfate and ATP in the Golgi apparatus. Trends Biochem. Sci. 22, 203-207.
6. Yurchenco, P.D. & Atkinson, P.H. (1977). Equilibration of fucosyl glycoprotein pools in HeLa cells. Biochemistry 16, 944-953.
7. Ginsburg, V. (1960). Formation of guanosine diphosphate L-fucose from guanosine diphosphate D-mannose. J. Biol. Chem. 235, 2196-2201.
8. Ginsburg, V. (1961). Studies on the biosynthesis of guanosine diphosphate L-fucose. J. Biol. Chem. 236, 2389-2393.
9. Sturla, L., Bisso, A., Zanardi, D., Benatti, U. & De Flora, A. (1997). Expression, purification and characterization of GDP-D-mannose 4,6 dehydratase from E. coli. FEBS Lett. 412, 126-130.
10. Sullivan, F.X., et al., & Cummings, D.A. (1998). Molecular cloning of human GDP-D-mannose 4,6-dehydratase and reconstitution of GDP-L-fucose biosynthesis in vitro. J. Biol. Chem. 273, 8193-8202.
11. Sturla, L., et al., & Tonetti, M. (1998). Defective intracellular activity of GDP-D-mannose 4,6 dehydratase in leucocyte adhesion deficiency type II syndrome. FEBS Lett. 429, 274-278.
12. Tonetti, M., Sturla, L., Bisso, A., Benatti, U. & De Flora A. (1996). Synthesis of GDP-L-fucose by the human protein FX. J. Biol. Chem. 271, 27274-27279.
13. Stevenson, G., Andrianopoulos, K., Hobbs, M. & Reeves, P.R. (1996). Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid. J. Bacteriol. 178, 4885-4893.
14. Tonetti, M., et al., & Bolognesi, M. (1998). Preliminary crystallographic investigation of recombinant GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from E. coli. Acta Cryst. D 54, 684-686.
15. Appelmelk, B.J., Negrini, R., Moran, A.P. & Kuipers, E.J. (1997). Molecular mimicry between Helicobacter pylori and the host. Trends Microbiol. 5, 70-73.
16. Jornvall, H., et al., & Gosh, D. Short-chain dehydrogenases/reductases (SDR). Biochemistry 34, 6004-6012.
17. Baker, M.E. & Blasco, R. (1992). Expansion of the mammalian 3-β-hydroxysteroid dehydrogenase/plant dihydroflavonol reductase superfamily to include a bacterial cholesterol dehydrogenase, a bacterial UDP-galactose-4-epimerase, and open reading frames in vaccinia virus and fish limphocystis disease virus. FEBS Lett. 301, 89-93.
18. Labesse, G., Vidal-Cros, A., Chomilier, J. Gaudry, M. & Mornon, J.-P. (1994). Structural comparisons lead to the definition of a new superfamily of NAD(P)(H)-accepting oxidoreductases: the single domain reductases/epimerases/dehydrogenases (the 'RED' family). Biochem.J. 304, 95-99.
19. Laskowski, R.A., Mac Arthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemistry of protein structures. J. Appl. Cryst. 26, 283-291.
20. Bauer, A.J., Rayment, I., Frey, P.A. & Holden, H.M. (1992). The molecular structure of UDP-galactose 4-epimerase from Escherichia coli determined at 2.5 Å resolution. Proteins 12, 372-381.
21. Thoden, J.B., Frey, P.A. & Holden, H.M. (1996). Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli. Biochemistry 35, 2557-2566.
22. Thoden, J.B., Frey, P.A. & Holden, H.M. (1996). High resolution structure of UDP-galactose 4-epimerase complexed with UDP-phenol. Protein Sci. 5, 2149-2161.
23. Thoden, J.B., Frey, P.A. & Holden, H.M. (1996). Molecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: implications for the catalytic mechanism. Biochemistry 35, 5137-5144.
24. Duax, W.L., Griffin, J.F. & Gosh, D. (1996). The fascinating complexities of steroid-binding enzymes. Curr. Opin. Struct. Biol. 6, 813-823.
25. Gosh, D., et al., & Lin, S-X. (1995). Structure of estrogenic 17β-hydroxysteroid dehydrogenase at 2.20 Å resolution. Structure 3, 503-513.
26. Tanaka, N., Nonaka, T., Nakanishi, M., Deyashiki, Y., Hara, A. & Mitsui, Y. (1996). Crystal structure of the ternary complex of mouse lung carbonyl reductase at 1.8 Å resolution: the structural origin of coenzyme specificity in the short-chain dehydrogenase/reductase family. Structure 4, 33-45.
27. Varughese, K.I., Xuong, N.H., Kiefer, P.M., Matthews, D.A. & Whiteley, J.M. (1994). Structural and mechanistic characteristics of dihydropteridine reductase: a member of the Tyr-(X)3-Lys-containing family of reductases and dehydrogenases. Proc. Natl Acad. Sci. USA 91, 5582-5586.
28. Azzi, A, Rehse, P.H., Zhu, D-W., Campbell, R.L., Labrie, F. & Lin, S-X. (1996). Crystal structure of human estrogenic 17β-hydroxysteroid dehydrogenase complexed with 17β-estradiol. Nat. Struct. Biol. 3, 665-668.
29. Lewis, M, et al., & Lu, P. (1996). Crystal structure of the lactose operon represser and its complexes with DNA and inducer. Science 271, 1247-1254.
30. Zou, J-Y., Flocco, M.M. & Mowbray, S.L (1993). The 1.7 Å refined structure of the periplasmic glucose/galactose receptor from Salmonella typhimurium. J. Mol. Biol. 233, 739-752.
31. Tanaka, N., Nonaka, T., Tanabe, T., Yoshimoto, T., Tsuru, D. & Mitsui, Y. (1996). Crystal structures of the binary and ternary complexes of 7α-hydroxysteroid dehydrogenases from Escherichia coli. Biochemistry 35, 7715-7730.
32. Gosh, D., Wawrzak, Z., Weeks, C.M., Duax, W.L. & Erman, M. (1994). The refined three-dimensional structure of 3α,20β-hydroxysteroid dehydrogenase and possible roles of the residues conserved in short-chain dehydrogenases. Structure 2, 629-640.
33. Bell, C.E., Yeates, T.O. & Eisenberg, D. (1997). Unusual conformation of nicotinamide adenine dinucleotide (NAD) bound to diphtheria toxin: a comparison with NAD bound to the oxidoreductase enzymes. Protein Sci. 6, 2084-209.
34. Persson, B., Krook, M. & Jornvall, H. (1991). Characteristics of short-chain alcohol dehydrogenases and related enzymes. Eur. J. Biochem. 200, 537-543.
35. Thoden, J.B., Gulick, A.M. & Holden, H.M. (1997). Molecular structures of the S124A, S124T, and S124T site-directed mutants of UDP-galactose 4-epimerase from Escherichia coli. Biochemistry 36, 10685-10695.
36. Thoden, J.B., Hegeman, A.D., Wesenperg, G., Chapeau, M.C., Frey. P.A. & Holden, H.M. (1997). Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli. Biochemistry 36, 6294-6304.
37. Swanson, B.A. & Frey, P.A. (1993). Identification of lysine 153 as a functionally important residue in UDP-galactose-4-epimerase from Escherichia coli. Biochemistry 32, 13231-13236.
38. Burke, J.R. & Frey, P.A. (1993). The importance of binding energy in catalysis of hydride transfer by UDP-galactose 4-epimerase: A 13C and 15N NMR and kinetic study. Biochemistry 32, 13220-12230.
39. Higgins, D.G. & Sharp, P.M. (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237-244.
40. Liu, Y., et al., & Frey, P.A. (1997). Mechanistic role of tyrosine 149 and serine 124 in UDP-galactose 4-epimerase from Escherichia coli. Biochemistry 36, 10675-10684.
41. Szikora, V.P., et al., & Boon. T. (1990). Structure of the gene of turn-transplantation antigen P35B: presence of a point mutation in the antigenic allele. EMBO J. 9, 1041-1050.
42. Leslie, A.G.W. (1992). Joint CCP4 and ESF-EACMB Newsletter in Protein Crystallography No. 26. SERC Daresbury Laboratory, Warrington, UK.
43. Collaborative Computational Project Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50, 760-763.
44. Sheldrick, G.M. (1991). Heavy atom location using SHELX-90. In Proceedings of the CCP4 study weekend: isomorphous replacement and anomalous scattering. pp. 23-38, SERC Daresbury Laboratory, Warrington, UK.
45. Otwinowski, Z. (1991). Maximum likelihood refinement of heavy atom parameters. In Isomorphous replacement and anomalous scattering, (Wolf, W., Evans, P.R. & Leslie, A.G.W, eds), pp. 80-86. Daresbury Laboratory, Warrington, UK.
46. Cowtan, K. & Main, P. (1998). Miscellaneous algorithms for density modification. Acta Cryst. D 54, 487-493.
47. Kleywegt, G.J. & Jones, T.A. (1997). Template convolution to enhance or detect structural features in macromolecular electron-density maps. Acta Cryst. D 53 179-185.
48. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building models in electron density maps and the location of errors in these models. Acta Cryst. A 47, 110-119.
49. Tronrud, D.E., Ten Eyck, L.F. & Matthews, B.W. (1987). An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Cryst. A 43, 489-501.
50. Engh, R.A. & Huber, R. (1991). Accurate bond angles and parameters for X-ray protein structure refinement. Acta Cryst. A 45, 392-400.
51. Brünger, A.T. (1992). The free R value: a novel statistical quantity for assessing the accuracy of crystal structure. Nature 355, 472-474.
52. Kabsh, W. & Sander, K. (1988). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded geometrical features. Biopolymers 22, 2577-2673.
53. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots for protein structures. J. Appl. Cryst. 24, 946-950.