Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway

Acta Crystallographica Section D: Biological Crystallography

Volumn 69, Issue 8, 2013, Pages 1567-1579

  Valegård, Karin ^a   Iqbal, Aman ^b   Kershaw, Nadia J ^b   Ivison, David ^b   Généreux, Catherine ^c   Dubus, Alain ^c   Blikstad, Cecilia ^d   Demetriades, Marina ^b   Hopkinson, Richard J ^b   Lloyd, Adrian J ^e   Roper, David I ^e   Schofield, Christopher J ^b   Andersson, Inger ^d   Mcdonough, Michael A ^b  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF LIÈGE   (Belgium)

^d UPPSALA UNIVERSITY   (Sweden)

^e UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

lactam antibiotics; lactamase fold; clavulanic acid biosynthesis pathway; esterases; penicillin binding proteins

Indexed keywords

BACTERIAL PROTEIN; BETA LACTAM; BETA LACTAMASE; CARBOXYPEPTIDASE; CEPHALOSPORIN DERIVATIVE; CLAVULANIC ACID; ESTERASE; PENICILLIN BINDING PROTEIN; PENICILLIN DERIVATIVE; SERINE;

Β-LACTAM ANTIBIOTICS; Β-LACTAMASE FOLD; ARTICLE; BIOSYNTHESIS; CHEMICAL STRUCTURE; CHEMISTRY; CLAVULANIC ACID BIOSYNTHESIS PATHWAY; ENZYME ACTIVE SITE; GENETICS; HYDROLYSIS; METABOLISM; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; STREPTOMYCES; X RAY CRYSTALLOGRAPHY;

Β-LACTAM ANTIBIOTICS; Β-LACTAMASE FOLD; CLAVULANIC ACID BIOSYNTHESIS PATHWAY; ESTERASES; PENICILLIN-BINDING PROTEINS;

AMINO ACID MOTIFS; BACTERIAL PROTEINS; BETA-LACTAMASES; BETA-LACTAMS; CARBOXYPEPTIDASES; CATALYTIC DOMAIN; CEPHALOSPORINS; CLAVULANIC ACID; CRYSTALLOGRAPHY, X-RAY; HYDROLYSIS; MODELS, MOLECULAR; PENICILLINS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SERINE; STREPTOMYCES;

EID: 84881306200     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444913011013     Document Type: Article

References (68)

1. Abrahams, K. A. (2011). Thesis. Warwick University, England.
2. Adam, M., Damblon, C., Jamin, M., Zorzi,W., Dusart, V., Galleni, M., el Kharroubi, A., Piras, G., Spratt, B. G., Keck, W., Coyette, J., Ghuysen, J-M., Nguyen-Distèche, M. & Frère, J-M. (1991). Biochem. J. 279, 601-604
3. Adam, M., Damblon, C., Plaitin, B., Christiaens, L. & Frère, J-M. (1990). Biochem. J. 270, 525-529
4. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221
5. Alexander, D. C. & Jensen, S. E. (1998). J. Bacteriol. 180, 4068-4079
6. Asano, Y., Mori, T., Hanamoto, S., Kato, Y. & Nakazawa, A. (1989). Biochem. Biophys. Res. Commun. 162, 470-474
7. Baggaley, K. H., Brown, A. G. & Schofield, C. J. (1997). Nat. Prod. Rep. 14, 309-333
8. Bompard-Gilles, C., Remaut, H., Villeret, V., Prangé, T., Fanuel, L., Delmarcelle, M., Joris, B., Frère, J. & Van Beeumen, J. (2000). Structure, 8, 971-980
9. Brown, R. P., Aplin, R. T. & Schofield, C. J. (1996). Biochemistry, 35, 12421-12432
10. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21
11. Chen, Y., Zhang, W., Shi, Q., Hesek, D., Lee, M., Mobashery, S. & Shoichet, B. K. (2009). J. Am. Chem. Soc. 131, 14345-14354
12. Clarke, T. B., Kawai, F., Park, S-Y., Tame, J. R. H., Dowson, C. G. & Roper, D. I. (2009). Biochemistry, 48, 2675-2683
13. Contreras-Martel, C., Job, V., Di Guilmi, A. M., Vernet, T., Dideberg, O. & Dessen, A. (2006). J. Mol. Biol. 355, 684-696
14. Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275
15. Egan, L. A., Busby, R.W., Iwata-Reuyl, D. & Townsend, C. A. (1997). J. Am. Chem. Soc. 119, 2348-2355
16. Fonzé, E., Vermeire, M., Nguyen-Distèche, M., Brasseur, R. & Charlier, P. (1999). J. Biol. Chem. 274, 21853-21860
17. Fuente, A. de la, Lorenzana, L. M., Martín, J. F. & Liras, P. (2002). J. Bacteriol. 184, 6559-6565
18. Galleni, M., Lamotte-Brasseur, J., Raquet, X., Dubus, A., Monnaie, D., Knox, J. R. & Frère, J-M. (1995). Biochem. Pharmacol. 49, 1171-1178
19. Ghuysen, J-M. (1991). Annu. Rev. Microbiol. 45, 37-67
20. Herzberg, O. & Moult, J. (1987). Science, 236, 694-701
21. Holm, L., Kääriäinen, S., Rosenströ m, P. & Schenkel, A. (2008). Bioinformatics, 24, 2780-2781
22. Holm, L. & Rosenströ m, P. (2010). Nucleic Acids Res. 38, W545-W549
23. Hutchinson, E. G. & Thornton, J. M. (1990). Proteins, 8, 203-212
24. Hutchinson, E. G. & Thornton, J. M. (1996). Protein Sci. 5, 212-220
25. Jelsch, C., Lenfant, F., Masson, J. M. & Samama, J-P. (1992). FEBS Lett. 299, 135-142
26. Jensen, S. E., Elder, K. J., Aidoo, K. A. & Paradkar, A. S. (2000). Antimicrob. Agents Chemother. 44, 720-726
27. Jensen, S. E., Paradkar, A. S.,Mosher, R. H., Anders, C., Beatty, P. H., Brumlik, M. J., Griffin, A. & Barton, B. (2004). Antimicrob. Agents Chemother. 48, 192-202
28. Jones, T. A., Zou, J-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119
29. Kallio, P., Sultana, A., Niemi, J., Mäntsälä, P. & Schneider, G. (2006). J. Mol. Biol. 357, 210-220
30. Kantola, J., Kunnari, T., Hautala, A., Hakala, J., Ylihonko, K. & Mäntsälä, P. (2000). Microbiology, 146, 155-163
31. Kelly, J. A., Dideberg, O., Charlier, P., Wery, J. P., Libert, M., Moews, P. C., Knox, J. R., Duez, C., Fraipont, C., Joris, B., Dusart, J., Frère, J-M. & Ghuysen, J-M. (1986). Science, 231, 1429-1431
32. Kelly, J. A. & Kuzin, A. P. (1995). J. Mol. Biol. 254, 223-236
33. Kershaw, N. J., Caines,M. E., Sleeman, M. C. & Schofield, C. J. (2005). Chem. Commun., pp. 4251-4263
34. Koch, A. L. (2000). Crit. Rev. Microbiol. 26, 205-220
35. Kuzin, A. P., Nukaga, M., Nukaga, Y., Hujer, A. M., Bonomo, R. A. & Knox, J. R. (1999). Biochemistry, 38, 5720-5727
36. La Fortelle, E. de & Bricogne, G. (1997). Methods Enzymol. 276, 472-494
37. Lamzin, V. S., Perrakis, A. &Wilson, K. S. (2001). International Tables for Crystallography, Vol. F, edited by M. G. Rossman & E. Arnold, pp. 720-722. Dordrecht: Kluwer Academic Publishers.
38. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291
39. Li, R., Khaleeli, N. & Townsend, C. A. (2000). J. Bacteriol. 182, 4087-4095
40. Lim, D. & Strynadka, N. C. (2002). Nature Struct. Biol. 9, 870-876
41. Llinás, A., Ahmed, N., Cordaro, M., Laws, A. P., Frère, J-M., Delmarcelle, M., Silvaggi, N. R., Kelly, J. A. & Page, M. I. (2005). Biochemistry, 44, 7738-7746
42. Lobkovsky, E., Billings, E. M., Moews, P. C., Rahil, J., Pratt, R. F. & Knox, J. R. (1994). Biochemistry, 33, 6762-6772
43. Massova, I. & Mobashery, S. (1998). Antimicrob. Agents Chemother. 42, 1-17
44. Maveyraud, L., Golemi, D., Kotra, L. P., Tranier, S., Vakulenko, S., Mobashery, S. & Samama, J-P. (2000). Structure, 8, 1289-1298
45. Mellado, E., Lorenzana, L. M., Rodriguez-Saiz, M., Diez, B., Liras, P. & Barredo, J. L. (2002). Microbiology, 148, 1427-1438
46. Minasov, G., Wang, X. & Shoichet, B. K. (2002). J. Am. Chem. Soc. 124, 5333-5340
47. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367
48. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). J. Mol. Biol. 247, 536-540
49. Negoro, S., Ohki, T., Shibata, N., Sasa, K., Hayashi, H., Nakano, H., Yasuhira, K., Kato, D., Takeo,M. & Higuchi, Y. (2007). J. Mol. Biol. 370, 142-156
50. Nicola, G., Peddi, S., Stefanova, M., Nicholas, R. A., Gutheil, W. G. & Davies, C. (2005). Biochemistry 44, 8207-8217
51. Okazaki, S., Suzuki, A., Komeda, H., Yamaguchi, S., Asano, Y. & Yamane, T. (2007). J. Mol. Biol. 368, 79-91
52. Otwinowski, Z. & Minor,W. (1997). Methods Enzymol. 276, 307-326
53. Pape, T. & Schneider, T. R. (2004). J. Appl. Cryst. 37, 843-844
54. Petersen, E. I., Valinger, G., Sö lkner, B., Stubenrauch, G. & Schwab, H. (2001). J. Biotechnol. 89, 11-25
55. Pratt, R. F. & McLeish, M. J. (2010). Biochemistry, 49, 9688-9697
56. Sauvage, E., Herman, R., Petrella, S., Duez, C., Bouillenne, F., Frère, J-M. & Charlier, P. (2005). J. Biol. Chem. 280, 31249-31256
57. Sauvage, E., Kerff, F., Terrak, M., Ayala, J. A. & Charlier, P. (2008). FEMS Microbiol. Rev. 32, 234-258
58. Silvaggi, N. R., Josephine, H. R., Kuzin, A. P., Nagarajan, R., Pratt, R. F. & Kelly, J. A. (2005). J. Mol. Biol. 345, 521-533
59. Strynadka, N. C., Adachi, H., Jensen, S. E., Johns, K., Sielecki, A., Betzel, C., Sutoh, K. & James, M. N. G. (1992). Nature (London), 359, 700-705
60. Sultana, A., Kallio, P., Jansson, A., Wang, J-S., Niemi, J., Mäntsälä, P. & Schneider, G. (2004). EMBO J. 23, 1911-1921
61. Tahlan, K., Park, H. U.,Wong, A., Beatty, P. H. & Jensen, S. E. (2004). Antimicrob. Agents Chemother. 48, 930-939
62. Torkkell, S., Kunnari, T., Palmu, K., Hakala, J., Mäntsälä , P. & Ylihonko, K. (2000). Antimicrob. Agents Chemother. 44, 396-399
63. Urbach, C., Evrard, C., Pudzaitis, V., Fastrez, J., Soumillion, P. & Declercq, J-P. (2009). J. Mol. Biol. 386, 109-120
64. Urbach, C., Fastrez, J. & Soumillion, P. (2008). J. Biol. Chem. 283, 32516-32526
65. Wagner, U. G., Petersen, E. I., Schwab, H. & Kratky, C. (2002). Protein Sci. 11, 467-478
66. Wilkin, J. M., Jamin, M., Damblon, C., Zhao, G-H., Joris, B., Duez, C. & Frère, J-M. (1993). Biochem. J. 291, 537-544
67. Zawadzke, L. E., Chen, C. C. H., Banerjee, S., Li, Z., Wäsch, S., Kapadia, G., Moult, J. & Herzberg, O. (1996). Biochemistry, 35, 16475-16482
68. Zhao, G., Meier, T. I., Kahl, S. D., Gee, K. R. & Blaszczak, L. C. (1999). Antimicrob. Agents Chemother. 43, 1124-1128