The 1.6 Å crystal structure of the AraC sugar-binding and dimerization domain complexed with D-Fucose

Journal of Molecular Biology

Volumn 273, Issue 1, 1997, Pages 226-237

  Soisson, Stephen M ^a   MacDougall Shackleton, Beth ^b   Schleif, Robert ^b   Wolberger, Cynthia ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Arabinose; AraC; Carbohydrate recognition; Convergent evolution; Fucose

Indexed keywords

ARABINOSE; BACTERIAL PROTEIN; CARBOHYDRATE BINDING PROTEIN; FUCOSE; REGULATOR PROTEIN; ARAC PROTEIN; ARAC PROTEIN, E COLI; ESCHERICHIA COLI PROTEIN; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; COMPARATIVE STUDY; COMPETITIVE INHIBITION; CRYSTAL STRUCTURE; DIMERIZATION; ESCHERICHIA COLI; EVOLUTION; GENE CONTROL; HYDROGEN BOND; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; CRYSTALLIZATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; STEREOISOMERISM; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ARABINOSE; ARAC TRANSCRIPTION FACTOR; BACTERIAL PROTEINS; BINDING SITES; CARBOHYDRATE CONFORMATION; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FUCOSE; GENE EXPRESSION REGULATION, BACTERIAL; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; REPRESSOR PROTEINS; STEREOISOMERISM; TRANSCRIPTION FACTORS;

EID: 0031576253     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1314     Document Type: Article

References (48)

1. Angyal S. J. Conformations of sugars. The Carbohydrates: Chemistry and Biochemistry. 1972;Academic Press, New York.
2. Beverin S., Sheppard D. E., Park S. S. DLEscherchia coliaraC. J. Bacteriol. 107:1971;79-86.
3. Boos W., Gordon A. S., Hall R. E., Price H. D. Transport properties of the galactose-binding protein ofEscherchia coli. J. Biol. Chem. 247:1972;917-924.
4. Brünger A. T. FreeR. Nature. 355:1992a;472-475.
5. Brünger A. T. X-PLOR v3.1. A System for X-ray Crystallography and NMR, Manual. 1992b;Yale University Press, New Haven.
6. Bustos S., Schleif R. Functional domains of the AraC protein. Proc. Natl Acad. Sci. USA. 90:1993;5638-5642.
7. Cygler M., Rose D. R., Bundle D. R. Recognition of a cell-surface oligosaccharide of pathogenicSalmonella. Science. 253:1991;442-445.
8. Doyle M. E., Brown C., Hogg R. W., Helling R. B. Induction of thearaEscherchia coli. J. Bacteriol. 110:1972;56-65.
9. Dunn T., Hahn S., Ogden S., Schleif R. An operator at -280 base pairs that is required for repression ofaraBAD. Proc. Natl Acad. Sci. USA. 81:1984;5017-5020.
10. Englesberg E., Irr J., Power J., Lee N. Positive control of enzyme synthesis by gene C in theL. J. Bacteriol. 90:1965;946-957.
11. Eustance R., Schleif R. The linker region of AraC protein. J. Bacteriol. 178:1996;7025-7030.
12. Eustance R., Bustos S., Schleif R. Reaching out: locating and lengthening the interdomain linker in AraC protein. J. Mol. Biol. 242:1994;330-338.
13. Evans S. V. SETOR. J. Mol. Graph. 11:1993;134-138.
14. Friedman A. M., Fischmann T. O., Steitz T. A. Crystal structure oflac. Science. 268:1995;1721-1727.
15. Greenblatt J., Schleif R. Arabinose C protein: regulation of the arabinose operonin vitro. Nature New Biol. 233:1971;166-170.
16. Hendrickson W., Schleif R. Regulation of theEscherchia coliL. J. Mol. Biol. 178:1984;611-628.
17. Hendrickson W., Schleif R. A dimer of AraC protein contacts three adjacent major groove regions of thearaI. Proc. Natl Acad. Sci. USA. 82:1985;3129-3133.
18. Jeffrey G. A., Lewis L. Cooperative aspects of hydrogen bonding in carbohydrates. Carbohydr. Res. 60:1978;179-182.
19. Jones T. A., Zou J. Y., Cowan S. W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect A. A47:1991;110-119.
20. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
21. 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.
22. Lauble H., Georgalis Y., Heinemann U. Studies on the domain structure of theSalmonella typhimurium. Eur. J. Biochem. 185:1989;319-325.
23. Lewis M., Chang G., Horton N. C., Kercher M. A., Pace H. C., Schumacher M. A., Brennen R. G., Lu P. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 271:1996;1247-1254.
24. Lobell R., Schleif R. DNA looping and unlooping by AraC protein. Science. 250:1990;528-532.
25. Luzzati V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallog. 5:1952;802-810.
26. Maenaka K., Kawai G., Watanabe K., Sunada F., Kumagai I. Functional and structural role of a tryptophan generally observed in protein-carbohydrate interaction. J. Biol. Chem. 269:1994;7070-7075.
27. Martin K., Huo L., Schleif R. The DNA loop model forarain vivo. Proc. Natl Acad. Sci. USA. 83:1986;3654-3658.
28. Miller D. M., Olson J. S., Quiocho F. A. The mechanism of sugar binding to the periplasmic receptor for galactose chemotaxis and transport inEscherchia coli. J. Biol. Chem. 255:1980;2465-2471.
29. Mowbray S. L., Cole L. B. 1.7 Å X-ray structure of the periplasmic ribose receptor from Escherichia coli. J. Mol. Biol. 225:1992;155-175.
30. Otwinowski, Z. 1993, Proceedings of the CCP4 Study Weekend: Data Collection and Processing.
31. Parsons R. G., Hogg R. W. Crystallization and characterization of theLEscherchia coli. J. Biol. Chem. 249:1974;3602-3607.
32. Pigman W., Anet E. F. L. J. Mutarotations and actions of acids and bases. Pigman W., Horton D. The Carbohydrates: Chemistry and Biochemistry. 1972;Academic Press, New York.
33. Quiocho F. A. Carbohydrate-binding proteins: tertiary structures and protein-sugar interactions. Annu. Rev. Biochem. 55:1986;287-315.
34. Quiocho F. A. Molecular features and basic understanding of protein-carbohydrate interactions: the arabinose-binding protein-sugar complex. Curr. Top. Microbiol. Immunol. 139:1988;135-148.
35. Quiocho F. A., Vyas N. K. Novel stereospecificity of theL. Nature. 310:1984;381-386.
36. Quiocho F. A., Gilliland G. L., Phillips G. N. The 2.8 Å resolution structure of theLEscherchia coli. J. Biol. Chem. 252:1977;5142-5149.
37. Quiocho F. A., Wilson D. K., Vyas N. K. Substrate specificity and affinity of a protein modulated by bound water molecules. Nature. 340:1989;404-407.
38. Schleif R. Two positively regulated systems,aramal. Neidhardt R. F. C. III, Ingraham J., Lin E., Low K., Magasanik B., Reznikoff W., Riley M., Schaechter M., Umbarger H. Escherichia coliSalmonella typhimurium. 1996;American Society for Microbiology, Washington.
39. Schumacher M. A., Choi K. Y., Zalkin H., Brennan R. G. Crystal structure of the LacI member, PurR, bound to DNA: minor groove binding by α helices. Science. 266:1994;763-770.
40. Soisson, S. M. 1997, Structural studies of the AraC protein from Escherichia coli, PhD thesis, Johns Hopkins School of Medicine, Baltimore, MD.
41. Soisson S. M., MacDougall-Shackleton B., Schleif R., Wolberger C. Structural basis for ligand-regulated oligomerization of AraC. Science. 276:1997;421-425.
42. Vyas N. K. Atomic features of protein-carbohydrate interactions. Curr. Opin. Strucut. Biol. 1:1991;732-740.
43. Vyas N. K., Vyas M. N., Quiocho F. A. Sugar and signal-transducer binding sites of theEscherchia coli. Science. 242:1988;1290-1295.
44. Wallace, R. G. 1982, AraC and its constitutive mutations in Escherichia coli in vitro, PhD thesis, University of California.
45. Wilcox G. The Interaction ofLD. J. Biol. Chem. 249:1974;6892-6894.
46. Wilcox G., Meuris P. Stabilization and size of the AraC protein. Mol. Gen. Genet. 145:1976;97-100.
47. Wilcox G., Meuris P., Bass R., Englesberg E. Regulation of theLin vitro. J. Biol. Chem. 249:1974;2946-2952.
48. Zhang X., Reeder T., Schleif R. Transcription activation parameters at ara pBAD. J. Mol. Biol. 258:1996;14-24.