Structures of shikimate dehydrogenase AroE and its paralog YdiB: A common structural framework for different activities

Journal of Biological Chemistry

Volumn 278, Issue 21, 2003, Pages 19463-19472

  Michel, Gurvan ^a   Roszak, Aleksander W ^b   Sauvé, Véronique ^a   Maclean, John ^b   Matte, Allan ^a   Coggins, John R ^b   Cygler, Miroslaw ^a   Lapthorn, Adrian J ^b,c  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CLOSED CONFORMATIONS;

AROMATIC COMPOUNDS; BIOSYNTHESIS; CONFORMATIONS; DRUG PRODUCTS; MICROORGANISMS; MOLECULAR STRUCTURE;

BIOCATALYSTS;

AROMATIC COMPOUND; NICOTINAMIDE ADENINE DINUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; SHIKIMATE DEHYDROGENASE; SHIKIMIC ACID DERIVATIVE; UNCLASSIFIED DRUG; ADENOSINE; ALCOHOL DEHYDROGENASE; NICOTINAMIDE; PYROPHOSPHATE; QUINATE DEHYDROGENASE; RECOMBINANT PROTEIN;

AROE GENE; ARTICLE; BACTERIAL GENE; BIOSYNTHESIS; CATALYSIS; CONFORMATIONAL TRANSITION; ESCHERICHIA COLI; GENE STRUCTURE; MICROORGANISM; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT; PRIORITY JOURNAL; PROTEIN EXPRESSION; SEQUENCE ANALYSIS; YDIB GENE; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; CRYSTALLIZATION; CRYSTALLOGRAPHY; DIMERIZATION; ENZYMOLOGY; HYDROGEN BOND; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; METAZOA; NEGIBACTERIA;

ADENOSINE; ALCOHOL OXIDOREDUCTASES; AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLIZATION; CRYSTALLOGRAPHY; DIMERIZATION; DIPHOSPHATES; ESCHERICHIA COLI; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NADP; NIACINAMIDE; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT;

EID: 0038265866     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M300794200     Document Type: Article

References (50)

1. Herrmann, K. M., and Weaver, L. M. (1999) Annu. Rev. Plant Physiol. Plant Mol. Biol. 50, 473-503
2. Roberts, F., Roberts, C. W., Johnson, J. J., Kyle, D. E., Krell, T., Coggins, J. R., Coombs, G. H., Milhous, W. K., Tzipori, S., Ferguson, D. J., Chakrabarti, D., and McLeod, R. (1998) Nature 393, 801-805
3. Kishore, G. M., and Shah, D. M. (1988) Annu. Rev. Biochem. 57, 627-663
4. Davies, G. M., Barrett-Bee, K. J., Jude, D. A., Lehan, M., Nichols, W. W., Pinder, P. E., Thain, J. L., Watkins, W. J., and Wilson, R. G. (1994) Antimicrob. Agents Chemother. 38, 403-406
5. Steinrücken, H. C., and Armhein, N. (1980) Biochem. Biophys. Res. Commun. 94, 1207-1212
6. Baerson, S. R., Rodriguez, D. J., Tran, M., Feng, Y., Biest, N. A., and Dill, G. M. (2002) Plant Physiol. 129, 1265-1275
7. Carpenter, E. P., Hawkins, A. R., Frost, J. W., and Brown, K. A. (1998) Nature 394, 299-302
8. Gourley, D. G., Shrive, A. K., Polikarpov, I., Krell, T., Coggins, J. R., Hawkins, A. R., Isaacs, N. W., and Sawyer, L. (1999) Nat. Struct. Biol. 6, 521-525
9. Romanowski, M. J., and Burley, S. K. (2002) Proteins 47, 558-562
10. Krell, T., Coggins, J. R., and Lapthorn, A. J. (1998) J. Mol. Biol. 278, 983-997
11. Schönbrunn, E., Eschenburg, S., Shuttleworth, W. A., Schloss, J. V., Amrhein, N., Evans, J. N., and Kabsch, W. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 1376-1380
12. Chaudhuri, S., and Coggins, J. R. (1985) Biochem. J. 226, 217-223
13. Anton, I. A., and Coggins, J. R. (1988) Biochem. J. 249, 319-326
14. Deka, R. K., Anton, I. A., Dunbar, B., and Coggins, J. R. (1994) FEBS Lett. 349, 397-402
15. Lambert, J. M., Boocock, M. R., and Coggins, J. R. (1985) Biochem. J. 226, 817-829
16. Hawkins, A. R., Lamb, H. K., Moore, J. D., Charles, I. G., and Roberts, C. F. (1993) J. Gen. Microbiol. 139, 2891-2899
17. Onrston, L. N., and Neidle, E. L. (2003) in The Biology of Acinetobacter (Tower, K., Bergogne-Berezin, E., and Fewson, C. A., eds) pp. 201-237, Plenum Publishing Corp., New York
18. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402
19. Maclean, J., Campbell, S. A., Pollock, K., Chackrewarthy, S., Coggins, J. R., and Lapthorn, A. J. (2000) Acta Crystallogr. Sect. D Biol. Crystallogr. 56, 512-515
20. Hendrickson, W. A., Horton, J. R., and LeMaster, D. M. (1990) EMBO J. 9, 1665-1672
21. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
22. Collaborative Computational Project, No. 4 (1994) Acta Crystallogr. Sect. D Biol. Crystallogr. 50, 760-763
23. Sheldrick, G. M. (1991) in Isomorphous Replacement and Anomalous Scattering (Wolf, W., Evans, P. R., and Leslie, A. G., eds) pp. 80-86, SERC Daresbury Laboratory, Warrington, UK
24. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. Sect. D Biol. Crystallogr. 53, 240-255
25. Perrakis, A., Morris, R., and Lamzin, V. S. (1999) Nat. Struct. Biol. 6, 458-463
26. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291
27. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. Sect. D Biol. Crystallogr. 54, 905-921
28. Jones, T. A., Zhou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crystallogr. Sect. A 47, 110-119
29. Geever, R. F., Huiet, L., Baum, J. A., Tyler, B. M., Patel, V. B., Rutledge, B. J., Case, M. E., and Giles, N. H. (1989) J. Mol. Biol. 207, 15-34
30. Hawkins, A. R., Lamb, H. K., Smith, M., Keyte, J. W., and Roberts, C. F. (1988) Mol. Gen. Genet. 214, 224-231
31. Holm, L., and Sander, C. (1993) J. Mol. Biol. 233, 123-138
32. Conte, L. L., Chothia, C., and Janin, J. (1999) J. Mol. Biol. 285, 2177-2198
33. Walkinshaw, M. D., Taylor, P., Sturrock, S. S., Atanasiu, C., Berge, T., Henderson, R. M., Edwardson, J. M., and Dryden, D. T. (2002) Mol. Cell 9, 187-194
34. Carugo, O., and Argos, P. (1997) Proteins 28, 10-28
35. Chakrabarti, P., and Samanta, U. (1995) J. Mol. Biol. 251, 9-14
36. Dansette, P., and Azerad, R. (1974) Biochimie (Paris) 56, 751-755
37. Roszak, A. W., Robinson, D. A., Krell, T., Hunter, I. S., Fredrickson, M., Abell, C., Coggins, J. R., and Lapthorn, A. J. (2002) Structure 10, 493-503
38. Balinsky, D., and Davies, D. D. (1961) Biochem. J. 80, 296-300
39. Bugg, T. D., Abell, C., and Coggins, J. R. (1988) Tetrahedron Lett. 29, 6779-6782
40. Fersht, A. R. (1988) Biochemistry 27, 1577-1580
41. Dennis, A. W., and Balinsky, D. (1972) Int. J. Biochem. 9, 93-102
42. Adams, M. J., Buehner, M., Chandrasekhar, K., Ford, G. C., Hackert, M. L., Liljas, A., Rossmann, M. G., Smiley, I. E., Allison, W. S., Everse, J., Kaplan, N. O., and Taylor, S. S. (1973) Proc. Natl. Acad. Sci. U. S. A. 70, 1968-1972
43. Andersson, P., Kvassman, J., Lindstrom, A., Olden, B., and Pettersson, G. (1981) Eur. J. Biochem. 113, 425-433
44. Krell, T., Chackrewarthy, S., Pitt, A. R., Elwell, A., and Coggins, J. R. (1998) J. Pept. Res. 51, 201-209
45. Chackrewarthy, S. (1996) Studies on the Active-site of Escherichia coli Shikimate Dehydrogenase. Ph.D. thesis, University of Glasgow
46. Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millan-Zarate, D., Diaz-Peredo, E., Sanchez-Solano, F., Perez-Rueda, E., Bonavides-Martinez, C., and Collado-Vides, J. (2001) Nucleic Acids Res. 29, 72-74
47. Carson, M. (1997) Methods Enzymol. 277, 493-505
48. Gouet, P., Courcelle, E., Stewart, D. I., and Metoz, F. (1999) Bioinformatics 15, 305-308
49. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950
50. Nicholls, A., Sharp, K. A., and Honig, B. (1991) Proteins Struct. Funct. Genet. 11, 281-296