The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis

Acta Crystallographica Section D: Biological Crystallography

Volumn 69, Issue 12, 2013, Pages 2543-2554

  Kumar, Atul ^a   Kumar, Sanjiv ^a   Kumar, Dilip ^a   Mishra, Arpit ^a   Dewangan, Rikeshwer P ^a   Shrivastava, Priyanka ^a   Ramachandran, Srinivasan ^a   Taneja, Bhupesh ^a  

^a NATIONAL CHEMICAL LABORATORY   (India)

Author keywords

fold; LC MS analysis; M. tuberculosis; N acetylmuramoyl l alanine amidase; Rv3717; SAD phasing

Indexed keywords

AMIDASE; N ACETYLMURAMOYLALANINE AMIDASE; PEPTIDOGLYCAN; ZINC;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; HUMAN; LC/MS ANALYSIS; M. TUBERCULOSIS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; MYCOBACTERIUM TUBERCULOSIS; PROTEIN CONFORMATION; RV3717; SAD PHASING; TUBERCULOSIS; X RAY CRYSTALLOGRAPHY; Α/Β-FOLD;

LC/MS ANALYSIS; M. TUBERCULOSIS; N-ACETYLMURAMOYL-L-ALANINE AMIDASE; RV3717; SAD PHASING; Α/Β-FOLD;

AMIDOHYDROLASES; AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PEPTIDOGLYCAN; PROTEIN CONFORMATION; TUBERCULOSIS; ZINC;

EID: 84889844744     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444913026371     Document Type: Article

References (56)

1. Allignet, J., Aubert, S., Dyke, K. G. & El Solh, N. (2001). Infect. Immun. 69, 712-718.
2. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Proc. Natl Acad. Sci. USA, 98, 10037-10041.
3. Berry, A. M., Lock, R. A., Hansman, D. & Paton, J. C. (1989). Infect. Immun. 57, 2324-2330.
4. Bhardwaj, A. et al. (2011). Tuberculosis, 91, 479-486.
5. Böth, D., Schneider, G. & Schnell, R. (2011). J. Mol. Biol. 413, 247-260.
6. Brennan, P. J. & Nikaido, H. (1995). Annu. Rev. Biochem. 64, 29-63.
7. Bricogne, G., Blanc, E., Brandl, M., Flensburg, C., Keller, P., Paciorek, W., Roversi, P., Sharff, A., Smart, O. S., Vonrhein, C. & Womack, T. O. (2011). BUSTER v.2.10.0. Cambridge: Global Phasing Ltd.
8. Buist, G., Kok, J., Leenhouts, K. J., Dabrowska, M., Venema, G. & Haandrikman, A. J. (1995). J. Bacteriol. 177, 1554-1563.
9. Carrasco-López, C., Rojas-Altuve, A., Zhang, W., Hesek, D., Lee, M., Barbe, S., André, I., Ferrer, P., Silva-Martin, N., Castro, G. R., Martínez-Ripoll, M., Mobashery, S. & Hermoso, J. A. (2011). J. Biol. Chem. 286, 31714-31722.
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. Deng, L. L., Humphries, D. E., Arbeit, R. D., Carlton, L. E., Smole, S. C. & Carroll, J. D. (2005). Biochim. Biophys. Acta, 1747, 57-66.
12. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
13. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
14. Evans, G. & Pettifer, R. (2001). J. Appl. Cryst. 34, 82-86.
15. Harding, M. M. (2001). Acta Cryst. D57, 401-411.
16. Heijenoort, J. van (2011). Microbiol. Mol. Biol. Rev. 75, 636-663.
17. Hett, E. C. & Rubin, E. J. (2008). Microbiol. Mol. Biol. Rev. 72, 126-156.
18. Hoffmann, C., Leis, A., Niederweis, M., Plitzko, J. M. & Engelhardt, H. (2008). Proc. Natl Acad. Sci. USA, 105, 3963-3967.
19. Jayaswal, R. K., Lee, Y.-I. & Wilkinson, B. J. (1990). J. Bacteriol. 172, 5783-5788.
20. Kaur, D., Berg, S., Dinadayala, P., Gicquel, B., Chatterjee, D., McNeil, M. R., Vissa, V. D., Crick, D. C., Jackson, M. & Brennan, P. J. (2006). Proc. Natl Acad. Sci. USA, 103, 13664-13669.
21. Korndörfer, I. P., Danzer, J., Schmelcher, M., Zimmer, M., Skerra, A. & Loessner, M. J. (2006). J. Mol. Biol. 364, 678-689.
22. Kumar, A., Saigal, K., Malhotra, K., Sinha, K. M. & Taneja, B. (2011). J. Biol. Chem. 286, 19652-19661.
23. Kumar, S., Puniya, B., Parween, S., Nahar, P. & Ramachandran, S. (2013). PLoS One, 8, e69790.
24. Leslie, A. G. W. & Powell, H. R. (2007). Evolving Methods for Macromolecular Crystallography, edited by R. J. Read & J. L. Sussman, pp. 41-51. Dordrecht: Springer.
25. Li, Z. S., Beveridge, T. J., Betts, J. & Clarke, A. J. (1999). Microbiology, 145, 169-176.
26. Loessner, M. J., Kramer, K., Ebel, F. & Scherer, S. (2002). Mol. Microbiol. 44, 335-349.
27. Lopez-Marin, L. M. (2012). Clin. Dev. Immunol. 2012, 917860.
28. Low, L. Y., Yang, C., Perego, M., Osterman, A. & Liddington, R. C. (2005). J. Biol. Chem. 280, 35433-35439.
29. Low, L. Y., Yang, C., Perego, M., Osterman, A. & Liddington, R. (2011). J. Biol. Chem. 286, 34391-34403.
30. Marchler-Bauer, A. et al. (2011). Nucleic Acids Res. 39, D225-D229.
31. Mayer, M. J., Garefalaki, V., Spoerl, R., Narbad, A. & Meijers, R. (2011). J. Bacteriol. 193, 5477-5486.
32. McNeil, M. R. & Brennan, P. J. (1991). Res. Microbiol. 142, 451-463.
33. Meroueh, S. O., Bencze, K. Z., Hesek, D., Lee, M., Fisher, J. F., Stemmler, T. L. & Mobashery, S. (2006). Proc. Natl Acad. Sci. USA, 103, 4404-4409.
34. Milohanic, E., Jonquières, R., Cossart, P., Berche, P. & Gaillard, J.-L. (2001). Mol. Microbiol. 39, 1212-1224.
35. 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.
36. Nguyen, L. & Thompson, C. J. (2006). Trends Microbiol. 14, 304-312.
37. Odintsov, S. G., Sabala, I., Marcyjaniak, M. & Bochtler, M. (2004). J. Mol. Biol. 335, 775-785.
38. Painter, J. & Merritt, E. A. (2006). Acta Cryst. D62, 439-450.
39. Panjikar, S., Parthasarathy, V., Lamzin, V. S., Weiss, M. S. & Tucker, P. A. (2005). Acta Cryst. D61, 449-457.
40. Panjikar, S., Parthasarathy, V., Lamzin, V. S., Weiss, M. S. & Tucker, P. A. (2009). Acta Cryst. D65, 1089-1097.
41. Pérez-Dorado, I., González, A., Morales, M., Sanles, R., Striker, W., Vollmer, W., Mobashery, S., García, J. L., Martínez-Ripoll, M., García, P. & Hermoso, J. A. (2010). Nature Struct. Mol. Biol. 17, 576-581.
42. Petersen, T. N., Brunak, S., von Heijne, G. & Nielsen, H. (2011). Nature Methods, 8, 785-786.
43. Potterton, E., Briggs, P., Turkenburg, M. & Dodson, E. (2003). Acta Cryst. D59, 1131-1137.
44. Punta, M. et al. (2012). Nucleic Acids Res. 40, D290-D301.
45. Raviglione, M., Marais, B., Floyd, K., Lönnroth, K., Getahun, H., Migliori, G. B., Harries, A. D., Nunn, P., Lienhardt, C., Graham, S., Chakaya, J., Weyer, K., Cole, S., Kaufmann, S. H. & Zumla, A. (2012). Lancet, 379, 1902-1913.
46. Ruggiero, A., Marasco, D., Squeglia, F., Soldini, S., Pedone, E., Pedone, C. & Berisio, R. (2010). Structure, 18, 1184-1190.
47. Rupp, M. E., Fey, P. D., Heilmann, C. & Götz, F. (2001). J. Infect. Dis. 183, 1038-1042.
48. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. & Wolfson, H. J. (2005). Nucleic Acids Res. 33, W363-W367.
49. Sharma, P., Yamini, S., Dube, D., Singh, A., Sinha, M., Dey, S., Mitra, D. K., Kaur, P., Sharma, S. & Singh, T. P. (2012). J. Biol. Chem. 287, 22153-22164.
50. Shida, T., Hattori, H., Ise, F. & Sekiguchi, J. (2001). J. Biol. Chem. 276, 28140-28146.
51. Smith, T. J., Blackman, S. A. & Foster, S. J. (2000). Microbiology, 146, 249-262.
52. Vollmer, W., Blanot, D. & de Pedro, M. A. (2008). FEMS Microbiol. Rev. 32, 149-167.
53. World Health Organization (2011). Global Tuberculosis Control. Geneva: World Health Organization. http://whqlibdoc.who.int/publications/2011/ 9789241564380-eng.pdf.
54. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
55. Yang, D. C., Tan, K., Joachimiak, A. & Bernhardt, T. G. (2012). Mol. Microbiol. 85, 768-781.
56. Zuber, B., Chami, M., Houssin, C., Dubochet, J., Griffiths, G. & Daffé, M. (2008). J. Bacteriol. 190, 5672-5680.