Structure and mechanism of L-Fucose Isomerase from Escherichia coli

Journal of Molecular Biology

Volumn 273, Issue 1, 1997, Pages 256-268

  Seemann, Joachim E ^a   Schulz, Georg E ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Ketol isomerase; Non crystallographic symmetry; Phase extension; Protein structure; X ray diffraction

Indexed keywords

BACTERIAL ENZYME; FUCOSE ISOMERASE; HYDROXYL GROUP; ISOMERASE; MANGANESE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN TERTIARY STRUCTURE; STEREOCHEMISTRY; X RAY DIFFRACTION;

EID: 0031576360     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1280     Document Type: Article

References (48)

1. Allen K. N., Lavie A., Farber G. K., Glasfeld A., Petsko G. A., Ringe D. Isotopic exchange plus substrate and inhibition kinetics ofD. Biochemistry. 33:1994;1481-1487.
2. Boulter J. R., Gielow W. O. Properties ofDEscherichia coli. J. Bacteriol. 113:1973;687-696.
3. Bourne Y., van Tilbeurgh H., Cambillau C. Protein-carbohydrate interactions. Curr. Opin. Struct. Biol. 3:1993;681-686.
4. Brosius J., Holy A. Regulation of the ribosomal RNA promoters with a syntheticlac. Proc. Natl Acad. Sci. USA. 81:1984;6929-6933.
5. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R-factor refinement by molecular dynamics. Science. 235:1987;458-460.
6. Carrell H. L., Glusker J. P., Burger V., Manfre F., Tritsch D., Biellmann J. -F. X-ray analysis ofD. Proc. Natl Acad. Sci. USA. 86:1989;4440-4444.
7. Carrell H. L., Hoier H., Glusker J. Modes of binding substrates and their analogues to the enzymeD. Acta Crystallog. sect. D. 50:1994;113-123.
8. Chen Y. -M., Zhu Y., Lin E. C. C. The organization of thefucLEscherichia coli. Mol. Gen. Genet. 210:1987;331-337.
9. Cleasby A., Wonacott A., Skarzynski T., Hubbard R. E., Davies G. J., Proudfoot A. E. I., Bernard A. R., Payton M. A., Wells T. N. C. The X-ray structure of phosphomannose isomerase fromCandida albicans. Nature Struct. Biol. 3:1996;470-479.
10. CCP4. Collaborative computational project number 4: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
11. Collyer C. A., Blow D. M. Observations of reaction intermediates and the mechanism of aldose-ketose interconversion byD. Proc. Natl Acad. Sci. USA. 87:1990;1362-1366.
12. Collyer C. A., Henrick K., Blow D. M. Mechanism for aldose-ketose interconversion byD. J. Mol. Biol. 212:1990;211-235.
13. Cowtan K. D. DM: an automatted procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newsletter Protein Crystallography. 31:1994;34-38.
14. Davenport R. C., Bash P. A., Seaton B. A., Karplus M., Petsko G. A., Ringe D. Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway. Biochemistry. 30:1991;5821-5826.
15. Diederichs K. Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm. Proteins: Struct. Funct. Genet. 23:1995;187-195.
16. Dreyer M. K. Überexpression, Reinigung, Kristallisation und röntgenographische Untersuchungen der LEscherichia coli LEscherichia coli. 1991;Albert-Ludwigs-Universität, Freiburg im Breisgau.
17. Dreyer M. K., Schulz G. E. The spatial structure of the class IILEscherichia coli. J. Mol. Biol. 231:1993;549-553.
18. Dreyer M. K., Schulz G. E. Catalytic mechanism of the metal-dependent fuculose aldolase fromEscherichia coli. J. Mol. Biol. 259:1996;458-466.
19. Eyrisch O. Chemoenzymatische Synthesen seltener und neuer Kohlenhydrate mit diversen Aldolasen, Isomerasen und Oxidoreduktasen. Dissertation. 1994;Albert-Ludwigs-Universität, Freiburg im Breisgau.
20. Farber G. K., Glasfeld A., Tiraby G., Ringe D., Petsko G. A. Crystallographic studies of the mechanism of xylose isomerase. Biochemistry. 28:1989;7289-7297.
21. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F. et al. Whole genome random sequencing and assembly ofHaemophilus influenzae. Science. 269:1995;469-512.
22. Flowers H. M. Chemistry and biochemistry ofDL. Advan. Carbohydr. Chem. Biochem. 39:1981;279-345.
23. Green M., Cohen S. Enzymatic conversion ofLL. J. Biol. Chem. 219:1956;557-568.
24. Jancarik J., Kim S.-H. Sparse matrix sampling: a screening method for crystallization of proteins. J. Appl. Crystallog. 24:1991;409-411.
25. Jones T. A., Zou J. Y., Cowan S. W., Kjeldgaard M. Improved methods of building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
26. Kabsch W. Evaluation of single crystal diffraction data from a position-sensitive detector. J. Appl. Crystallog. 21:1988;916-924.
27. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
28. Kleywegt G. J., Jones T. A. Halloween...masks and bones. From First Map to Final Model. 1994;SERC Daresbury Laboratory, Warrington.
29. 2+. J. Mol. Biol. 270:1997;1-7.
30. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
31. Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
32. Lavie A., Allen K. N., Petsko G. A., Ringe D. X-ray crystallographic structures ofD. Biochemistry. 33:1994;5469-5480.
33. Lolis E., Petsko G. A. Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-Å resolution: implications for catalysis. Biochemistry. 29:1990;6619-6625.
34. Luzzati V. Traitement statistique des erreurs dans la détermination des structures cristallines. Acta Crystallog. 5:1952;802-810.
35. Mande S. C., Mainfroid V., Kalk K. H., Goraj K., Martial J. A., Hol W. G. J. Crystal structure of recombinant human triosephosphate isomerase at 2.8 Å resolution. Triosephosphate isomerase-related human genetic disorders and comparison with the trypanosomal enzyme. Protein Sci. 3:1994;810-821.
36. Meyer J. E. W. Kristallstruktur und Permeationsmechanismus des Maltoporins aus Salmonella typhimurium. 1997;Albert-Ludwigs-Universität, Freiburg im Breisgau.
37. Meyer J. E. W., Schulz G. E. Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide-protein interactions. Protein Sci. 6:1997;1084-1091.
38. Nicholls A., Sharp K. A., Honig B. Protein folding and association: Insights from the interfacial and thermodynamical properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11:1991;281-296.
39. Oliver E. J., Mortlock R. P. Metabolism ofDAerobacter aerogenes. J. Bacteriol. 108:1971;293-299.
40. Otwinowsky Z. Oscillation data reduction program. Sawyer L., Isaacs N., Bailey S. Data Collection and Processing. 1993;SERC Daresbury Laboratory, Warrington.
41. Read R. J. Structure factor probabilities for related structures. Acta Crystallog. sect. A. 46:1990;900-912.
42. Rieder S. V., Rose I. A. The mechanism of the triosephosphate isomerase reaction. J. Biol. Chem. 234:1959;1007-1010.
43. Schulz G. E. Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2:1992;61-67.
44. Shaw P. J., Muirhead H. Crystallographic structure analysis of glucose-6-phosphate isomerase at 3.5 Å resolution. J. Mol. Biol. 109:1977;475-485.
45. Tong L., Rossmann M. G. The locked rotation function. Acta Crystallog. sect. A. 46:1990;783-792.
46. Vonrhein C. Struktur der Adenylatkinase aus Sulfolobus acidocaldarius. 1997;Albert-Ludwigs-Universität, Freiburg im Breisgau.
47. Vyas N. K. Atomic features of protein-carbohydrate interactions. Curr. Opin. Struct. Biol. 1:1991;732-740.
48. Whitlow M., Howard A. J., Finzel B. C., Poulos T. L., Winborne E., Gilliland G. L. A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 ÅStreptomyces rubiginosusD. Proteins: Struct. Funct. Genet. 9:1991;153-173.