The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: Catalysis with a twist

Structure

Volumn 8, Issue 5, 2000, Pages 453-462

  Deacon, A M ^a   Ni, Y S ^b   Coleman Jr , W G ^b   Ealick, S E ^a  

^a Cornell University ^*  (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

ADP L glycero D mannoheptose; Epimerase; Lipopolysaccharide core biosynthesis; Multiwavelength anomalous diffraction

Indexed keywords

ANTIBIOTIC AGENT; EPIMERASE; GLYCEROL; HEPTOSE; LIPOPOLYSACCHARIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE;

ARTICLE; BACTERIAL OUTER MEMBRANE; BIOSYNTHESIS; CATALYSIS; CRYSTAL STRUCTURE; ENZYME MECHANISM; ENZYME STRUCTURE; GRAM NEGATIVE BACTERIUM; MEMBRANE PERMEABILITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN;

BACTERIA (MICROORGANISMS); MAMMALIA; NEGIBACTERIA;

EID: 0034658405     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)00128-3     Document Type: Article

References (34)

1. Adams, G.A., Quadling, C. & Perry, M.B. (1967). D-Glycero-D-mannoheptose as a component of lipopolysaccharides from Gram-negative bacteria. Can. J. Microbiol. 13, 1605-1613.
2. Coleman, W.G., Jr. & Leive, L. (1979). Two mutations which affect the barrier function of the Escherichia coli K-12 outer membrane. J. Bacteriol. 139, 899-910.
3. Vaara, M. (1993). Outer membrane permeability barrier to azithromycin, clarithromycin, and roxithromycin in Gram-negative enteric bacteria. Antimicrob. Agents Chemother. 37, 354-356.
4. Taylor, P.W. (1983). Bactericidal and bacteriolytic activity of serum against Gram-negative bacteria. Microbiol. Rev. 47, 46-83.
5. Eidel, L. & Osborn, M.J. (1974). Phosphoheptose isomerase, first enzyme in biosynthesis of aldoheptose in Salmonella typhymurium. J. Biol. Chem. 249, 5642-5648.
6. Raetz, C.R.H. (1990). Biochemistry of endotoxins. Annu. Rev. Biochem. 59, 129-170.
7. Coleman, W.G., Jr. (1983). The rfaD gene codes for ADP-L-glycero-D-mannoheptose 6-epimerase, an enzyme required for lipopolysaccharide core biosynthesis. J. Biol. Chem. 259, 1985-1990.
8. Pegues, J.C., Chen, L., Gordon, A., Ding, L. & Coleman, W.G., Jr. (1990). Cloning, expression, and characterization of the Escherichia coli K-12 rfaD gene. J. Bacteriol. 172, 4652-4660.
9. Wierenga, R.K., Terpstra, P. & Hol, W.G.J. (1986). Prediction of the occurrence of the ADP-binding βαβ-fold in proteins using an amino acid sequence fingerprint. J.Mol. Biol. 187, 101-107.
10. Ding, L., Seto, B.L., Ahmed, S.A. & Coleman, W.G., Jr. (1994). Purification and properties of the Escherichia coli K-12 NAD-dependent nucleotide diphosphosugar epimerase, ADP-L-glycero-D-mannoheptose 6-epimerase. J. Biol. Chem. 269, 24384-24390.
11. Ding, L., et al., & Coleman, W.G., Jr. (1999). Crystallization and preliminary X-ray diffraction studies of the lipopolysaccharide core biosynthetic enzyme ADP-L-glycero-D-mannoheptose 6-epimerase from E. coli K-12. Acta Crystallogr. D 55, 685-688.
12. Tong, L. & Rossmann, M.G. (1990). The locked rotation function. Acta Crystallogr. A 46, 783-792.
13. Matthews, B.W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
14. Weeks, C.M. & Miller, R. (1999). The design and implementation of SnB version 2.0. J. Appl. Crystallogr. 32, 120-124.
15. Blessing R.H., Guo D.Y. & Langs DA (1996). Statistical expectation value of the Debye-Waller factor and E(hkl) values for macromolecular crystals. Acta Crystallogr. D 52, 257-266.
16. Blessing, R.H. & Smith, G.D. (1999). Difference structure factor normalization for heavy atom or anomaous scattering substructure determinations. J. Appl. Crystallogr. 32, 664-670.
17. Hauptman, H.A. (1991). A minima principle in the phase problem. In Crystallographic Computing 5: From Chemistry to Biology. (Moras, D., Podjarny, A.D. & Thierry, J.C. eds), pp. 324-332, IUCr and Oxford University Press, Oxford, UK.
18. Otwinowski, Z. (1991). Maximum-likelihood refinement of heavy atom parameters. In Proceedings of the CCP4 Study Weekend: Isomorphous Replacement and Anomaous Scattering. (Wolf, W., Evans, P.R. & Leslie, A.G.W., eds), pp. 80-88, SERC Proceedings, Daresbury Laboratories, Warrington, UK.
19. Cowtan, K.D. & Main, P. (1996). Phase combination and cross validation in iterated density-modification caculations. Acta Crystallogr. D 52, 43-48.
20. Deacon, A.M. & Ealick, S.E. (1999). Se-based MAD phasing: setting the sites on larger structures. Structure 7, R161-R166.
21. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
22. Rossmann, M.G., Moras, D. & Olsen, K.W. (1974). Chemica and biological evolution of a nucleotide-binding domain. Nature 250, 194-199.
23. 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.
24. Rizzi, M., et al., & Bolognesi, M. (1998). GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from Escherichia coli, a key enzyme in the biosynthesis of GDP-L-fucose, displays the structura characteristics of the RED protein homology superfamiiy. Structure 6, 1453-1465.
25. Somers, W.S., Stahl, M.L. & Sullivan, F.X. (1998). GDP-fucose synthetase from Escherichia coli: structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site. Structure 6, 1601-1612.
26. Thoden, J.B. & Holden, H.M. (1998). Dramatic differences in the binding of UDP-galactose and UDP-glucose to UDP-galactose 4-epimerase from Escherichia coli. Biochemistry 37, 11469-11477.
27. Hendrickson, W.A., Horton, J.R. & LeMaster, D.M. (1990). Selenomethionyl protein produced for analysis by multiwavelength anomaous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665-1672.
28. Leslie, A.G.W., Brick, P. & Wonacott, AT. (1986). An improved package for the measurement of oscillation photographs. Daresbury Laboratory Information Quart. Protein Crystallogr. 18, 33-39.
29. Evans, P.R. (1993). Data reduction. In Proceedings of the CCP4 Study Weekend: Data Collection and Processing, pp. 114-122.
30. Kleywegt, G.J. & Jones, T.A. (1994). Halloween ... mask and bones. In From First Map to Final Model. (Bailey, S., Hubbard, R. & Waller, D., eds), pp. 59-66, SERC Daresbury Laboratory, Warrington, UK.
31. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119.
32. Brünger, AT., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science 235, 458-460.
33. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
34. Nicholls, A., Sharp, K. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.