Structure and functional analysis of RifR, the type II thioesterase from the rifamycin biosynthetic pathway

Journal of Biological Chemistry

Volumn 284, Issue 8, 2009, Pages 5021-5029

  Claxton, Heather B ^a,b   Akey, David L ^a   Silver, Monica K ^b   Admiraal, Suzanne J ^b   Smith, Janet L ^a,b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL-COA; ACTIVE SITE; ACYL CARRIER; AMYCOLATOPSIS MEDITERRANEI; BIOSYNTHETIC PATHWAY; HOUSEKEEPING FUNCTIONS; KINETIC ANALYSIS; MALONYL-COA; NATURAL PRODUCTS; NONRIBOSOMAL PEPTIDE; RIFAMYCIN; STEADY-STATE KINETICS; STRUCTURAL SIMILARITY; SYNTHASE; THIOESTERASE; THIOESTERASES; TYPE II;

AMINES; BIOSYNTHESIS; HYDROLYSIS; SUBSTRATES;

CRYSTAL STRUCTURE;

ACYL COENZYME A; MALONYL COENZYME A; METHYLMALONYL COENZYME A MUTASE; PANTETHEINE PHOSPHATE; PEPTIDE SYNTHASE; POLYKETIDE SYNTHASE; PROPIONYL COENZYME A; PROTEIN RIFR; RIFAMYCIN; THIOL ESTER HYDROLASE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; FATTY ACID SYNTHASE; THIOESTERASE II;

ARTICLE; BIOSYNTHESIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DECARBOXYLATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME KINETICS; ENZYME MODIFICATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SYNTHESIS; MOLECULAR MIMICRY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN HYDROLYSIS; STEADY STATE; ACTINOMYCETALES; CHEMISTRY; ENZYMOLOGY; KINETICS; METABOLISM; PHYSIOLOGY; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

AMYCOLATOPSIS MEDITERRANEI;

ACTINOMYCETALES; ACYL COENZYME A; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; FATTY ACID SYNTHETASE COMPLEX; KINETICS; POLYKETIDE SYNTHASES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RIFAMYCINS; THIOLESTER HYDROLASES;

EID: 64149117037     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M808604200     Document Type: Article

References (56)

1. Yu, T.-W., Shen, Y., Doi-Katayama, Y., Tang, L., Park, C., Moore, B. S., Richard Hutchinson, C., and Floss, H. G. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 9051-9056
2. Weissman, K. J. (2004) Philos. Transact. A Math Phys. Eng. Sci. 362, 2671-2690
3. Hutchinson, C. R. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 3010-3012
4. Roongsawang, N., Washio, K., and Morikawa, M. (2007) ChemBioChem 8, 501-512
5. Heathcote, M. L., Staunton, J., and Leadlay, P. F. (2001) Chem. Biol. 8, 207-220
6. Schwarzer, D., Mootz, H. D., Linne, U., and Marahiel, M. A. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 14083-14088
7. Yeh, E., Kohli, R. M., Bruner, S. D., and Walsh, C. T. (2004) ChemBioChem 5, 1290-1293
8. Linne, U., Schwarzer, D., Schroeder, G. N., and Marahiel, M. A. (2004) Eur. J. Biochem. 271, 1536-1545
9. Libertini, L. J., and Smith, S. (1978) J. Biol. Chem. 253, 1393-1401
10. Chen, H., Hubbard, B. K., O'Connor, S. E., and Walsh, C. T. (2002) Chem. Biol. 9, 103-112
11. Chen, H., and Walsh, C. T. (2001) Chem. Biol. 8, 301-312
12. Fujimori, D. G., Hrvatin, S., Neumann, C. S., Strieker, M., Marahiel, M. A., and Walsh, C. T. (2007) Proc. Natl. Acad. Sci. U. S. A. 104, 16498-16503
13. Patel, J., Hoyt, J. C., and Parry, R. J. (1998) Tetrahedron 54, 15927-15936
14. Butler, A. R., Bate, N., and Cundliffe, E. (1999) Chem. Biol. 6, 287-292
15. Xue, Y., Zhao, L., Liu, H. W., and Sherman, D. H. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 12111-12116
16. Schneider, A., and Marahiel, M. A. (1998) Arch. Microbiol. 169, 404-410
17. Chen, S., Roberts, J. B., Xue, Y., Sherman, D. H., and Reynolds, K. A. (2001) Gene (Amst.) 263, 255-264
18. Wertheimer, A. M., Verweij, W., Chen, Q., Crosa, L. M., Nagasawa, M., Tolmasky, M. E., Actis, L. A., and Crosa, J. H. (1999) Infect. Immun. 67, 6496-6509
19. Geoffroy, V. A., Fetherston, J. D., and Perry, R. D. (2000) Infect. Immun. 68, 4452-4461
20. Hu, Z., Pfeifer, B. A., Chao, E., Murli, S., Kealey, J., Carney, J. R., Ashley, G., Khosla, C., and Hutchinson, C. R. (2003) Microbiology 149, 2213-2225
21. Reimmann, C., Patel, H. M., Walsh, C. T., and Haas, D. (2004) J. Bacteriol. 186, 6367-6373
22. Cosmina, P., Rodriguez, F., de Ferra, F., Grandi, G., Perego, M., Venema, G., and van Sinderen, D. (1993) Mol. Microbiol. 8, 821-831
23. Roberts, G. A., Staunton, J., and Leadlay, P. F. (1993) Eur. J. Biochem. 214, 305-311
24. Yu, F.-M., Qiao, B., Zhu, F., Wu, J.-C., and Yuan, Y.-J. (2006) Appl. Biochem. Biotechnol. 135, 145-158
25. Doi-Katayama, Y., Yoon, Y. J., Choi, C.-Y., Yu, T.-W., Floss, H. G., and Hutchinson, C. R. (2000) J. Antibiot. 53, 484-495
26. Kotowska, M., Pawlik, K., Butler, A. R., Cundliffe, E., Takano, E., and Kuczek, K. (2002) Microbiology 148, 1777-1783
27. Kim, B. S., Cropp, T. A., Beck, B. J., Sherman, D. H., and Reynolds, K. A. (2002) J. Biol. Chem. 277, 48028-48034
28. Tang, Y., Koppisch, A. T., and Khosla, C. (2004) Biochemistry 43, 9546-9555
29. Tsai, S. C., Lu, H., Cane, D. E., Khosla, C., and Stroud, R. M. (2002) Biochemistry 41, 12598-12606
30. Tsai, S.-C., Miercke, L. J. W., Krucinski, J., Gokhale, R., Chen, J. C. H., Foster, P. G., Cane, D. E., Khosla, C., and Stroud, R. M. (2001) Proc. Natl. Acad. Sci. U. S. A. 98, 14808-14813
31. Bruner, S. D., Weber, T., Kohli, R. M., Schwarzer, D., Marahiel, M. A., Walsh, C. T., and Stubbs, M. T. (2002) Structure 10, 301-310
32. Samel, S. A., Wagner, B., Marahiel, M. A., and Essen, L.-O. (2006) J. Mol. Biol. 359, 876-889
33. Chakravarty, B., Gu, Z., Chirala, S. S., Wakil, S. J., and Quiocho, F. A. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 15567-15572
34. Frueh, D. P., Arthanari, H., Koglin, A., Vosburg, D. A., Bennett, A. E., Walsh, C. T., and Wagner, G. (2008) Nature 454, 903-906
35. Koglin, A., Lohr, F., Bernhard, F., Rogov, V. V., Frueh, D. P., Strieter, E. R., Mofid, M. R., Guntert, P., Wagner, G., Walsh, C. T., Marahiel, M. A., and Dotsch, V. (2008) Nature 454, 907-911
36. Sambrook, J., Fritsch, E. F., and and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
37. Hoover, D. M., and Lubkowski, J. (2002) Nucleic Acids Res. 30, e43
38. Gokhale, R. S., Tsuji, S. Y., Cane, D. E., and Khosla, C. (1999) Science 284, 482-485
39. Tsuji, S. Y., Cane, D. E., and Khosla, C. (2001) Biochemistry 40, 2326-2331
40. Gasteiger, E., Hoogland, C., Gattiker, A., Durand, S., Wilkins, M. R., Appel, R. D., and Bairoch, A. (2005) in The Proteomics Protocols Handbook (Walker, J. M., ed) pp. 571-607, Humana Press, Totowa, NJ
41. Guerrero, S. A., Hecht, H. J., Hofmann, B., Biebl, H., and Singh, M. (2001) Appl. Microbiol. Biotechnol. 56, 718-723
42. Deutsch, J., Rapoport, S. I., and Rosenberger, T. A. (2002) Neurochem. Res. 27, 1577-1582
43. Lambalot, R. H., Gehring, A. M., Flugel, R. S., Zuber, P., LaCelle, M., Marahiel, M. A., Reid, R., Khosla, C., and Walsh, C. T. (1996) Chem. Biol. 3, 923-936
44. Quadri, L. E., Weinreb, P. H., Lei, M., Nakano, M. M., Zuber, P., and Walsh, C. T. (1998) Biochemistry 37, 1585-1595
45. Otwinowski, Z., and Minor, V. (1997) Methods Enzymol. 276, 307-326
46. Terwilliger, T. C., and Berendzen, J. (1999) Acta Crystallogr. Sect. D Biol. Crystallogr. 55, 849-861
47. Terwilliger, T. C. (2003) Acta Crystallogr. Sect. D Biol. Crystallogr. 59, 38-44
48. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. Sect. D Biol. Crystallogr. 60, 2126-2132
49. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. Sect. D Biol. Crystallogr. 53, 240-255
50. Collaborative Computational Project, Number 4 (1994) Acta Crystallogr. D50, 760-763
51. Painter, J., and Merritt, E. (2006) J. Appl. Crystallogr. 39, 109-111
52. Navaza, J. (1994) Acta Crystallogr. Sect. A Found. Crystallogr. 50, 157-163
53. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., III, Snoeyink, J., Richardson, J. S., and Richardson, D. C. (2007) Nucleic Acids Res. 35, 375-383
54. Frishman, D., and Argos, P. (1995) Proteins 23, 566-579
55. Heinig, M., and Frishman, D. (2004) Nucleic Acids Res. 32, 500-502
56. Akey, D. L., Kittendorf, J. D., Giraldes, J. W., Fecik, R. A., Sherman, D. H., and Smith, J. L. (2006) Nat. Chem. Biol. 2, 537-542