The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

Acta Crystallographica Section F: Structural Biology and Crystallization Communications

Volumn 66, Issue 10, 2010, Pages 1265-1273

  Das, Debanu ^a,b   Finn, Robert D ^c   Carlton, Dennis ^a,d   Miller, Mitchell D ^a,b   Abdubek, Polat ^a,e   Astakhova, Tamara ^a,f   Axelrod, Herbert L ^a,b   Bakolitsa, Constantina ^a,g   Chen, Connie ^a,e   Chiu, Hsiu Ju ^a,b   Chiu, Michelle ^a,e   Clayton, Thomas ^a,d   Deller, Marc C ^a,d   Duan, Lian ^a,f   Ellrott, Kyle ^a,f   Ernst, Dustin ^a,e   Farr, Carol L ^a,d   Feuerhelm, Julie ^a,e   Grant, Joanna C ^a,e   Grzechnik, Anna ^a,d   Han, Gye Won ^a,d   Jaroszewski, Lukasz ^a,f,g   Jin, Kevin K ^a,b   Klock, Heath E ^a,e   Knuth, Mark W ^a,e   Kozbial, Piotr ^a,g   Krishna, S Sri ^a,f,g   Kumar, Abhinav ^a,b   Marciano, David ^a,d   McMullan, Daniel ^a,e   Morse, Andrew T ^a,f   Nigoghossian, Edward ^a,e   Nopakun, Amanda ^a,d   Okach, Linda ^a,e   Puckett, Christina ^a,e   Reyes, Ron ^a,b   Rife, Christopher L ^a,b   Sefcovic, Natasha ^a,g   Tien, Henry J ^a,d   Trame, Christine B ^a,b   Van Den Bedem, Henry ^a,b   Weekes, Dana ^a,g   Wooten, Tiffany ^a,e   Xu, Qingping ^a,b   Hodgson, Keith O ^a,h   Wooley, John ^a,f   Elsliger, Marc André ^a,d   Deacon, Ashley M ^a,b   Godzik, Adam ^a,f,g   Lesley, Scott A ^a,d,e   Wilson, Ian A ^a,d   more..

^a Joint Center for Structural Genomics   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

^e GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g BURNHAM INSTITUTE   (United States)

^h SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

lactamase inhibitor protein like fold; BVU2987; DUF2874; human gut microbiome; PF11396; putative inhibitor proteins

Indexed keywords

PERIPLASMIC PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTEROIDES; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BACTEROIDES; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PERIPLASMIC PROTEINS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

BACTERIA (MICROORGANISMS); BACTEROIDES VULGATUS;

EID: 77958073342     PISSN: 17443091     EISSN: 17443091     Source Type: Journal    
DOI: 10.1107/S1744309109046788     Document Type: Article

References (66)

1. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Nucleic Acids Res. 25, 3389-3402.
2. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. (2001). Proc. Natl Acad. Sci. USA, 98, 10037-10041.
3. Boland, F. M., Atrih, A., Chirakkal, H., Foster, S. J. & Moir, A. (2000). Microbiology, 146, 57-64.
4. Chanal, C., Sirot, D., Romaszko, J. P., Bret, L. & Sirot, J. (1996). J. Antimicrob. Chemother. 38, 127-132.
5. Cohen, A. E., Ellis, P. J., Miller, M. D., Deacon, A. M. & Phizackerley, R. P. (2002). J. Appl. Cryst. 35, 720-726.
6. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
7. Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
8. Davis, I. W., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2004). Nucleic Acids Res. 32, W615-W619.
9. DeLano, W. L. (2008). PyMOL Molecular Viewer. DeLano Scientific LLC, Palo Alto, California, USA. http://www.pymol.org.
10. Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275.
11. Dolinsky, T. J., Czodrowski, P., Li, H., Nielsen, J. E., Jensen, J. H., Klebe, G. & Baker, N. A. (2007). Nucleic Acids Res. 35, W522-W525.
12. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
13. Finn, R. D., Tate, J., Mistry, J., Coggill, P. C., Sammut, S. J., Hotz, H. R., Ceric, G., Forslund, K., Eddy, S. R., Sonnhammer, E. L. & Bateman, A. (2008). Nucleic Acids Res. 36, D281-D288.
14. Frank, D. N. & Pace, N. R. (2008). Curr. Opin. Gastroenterol. 24, 4-10.
15. Gonzá lez, A. (2003a). Acta Cryst. D59, 315-322.
16. Gonzá lez, A. (2003b). Acta Cryst. D59, 1935-1942.
17. Goodstadt, L. & Ponting, C. P. (2001). Bioinformatics, 17, 845-846.
18. Hartshorn, M. J. (2002). J. Comput. Aided Mol. Des. 16, 871-881.
19. Hiniker, A., Collet, J. F. & Bardwell, J. C. (2005). J. Biol. Chem. 280, 33785-33791.
20. Holm, L., Kaariainen, S., Rosenstrom, P. & Schenkel, A. (2008). Bioinformatics, 24, 2780-2781.
21. Holm, L. & Park, J. (2000). Bioinformatics, 16, 566-567.
22. Kall, L., Krogh, A. & Sonnhammer, E. L. (2004). J. Mol. Biol. 338, 1027-1036.
23. Kang, S. G., Park, H. U., Lee, H. S., Kim, H. T. & Lee, K. J. (2000). J. Biol. Chem. 275, 16851-16856.
24. Katoh, K., Kuma, K., Toh, H. & Miyata, T. (2005). Nucleic Acids Res. 33, 511-518.
25. Kinross, J. M., von Roon, A. C., Holmes, E., Darzi, A. & Nicholson, J. K. (2008). Curr. Gastroenterol. Rep. 10, 396-403.
26. Kleywegt, G. J. (2000). Acta Cryst. D56, 249-265.
27. Klock, H. E., Koesema, E. J., Knuth, M.W. & Lesley, S. A. (2008). Proteins, 71, 982-994.
28. Krishna, S. S.,Weekes, D., Bakolitsa, C., Elsliger, M.-A.,Wilson, I. A., Godzik, A. & Wooley, J. (2010). Acta Cryst. F66, 1143-1147.
29. Krissinel, E. & Henrick, K. (2005). Computational Life Sciences, edited by M. R. Berthold, R. Glen, K. Diederichs, O. Kohlbacher & I. Fischer, pp. 163-174. Berlin: Springer-Verlag.
30. Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. (2008). Nature Protoc. 3, 1171-1179.
31. Laskowski, R. A., Chistyakov, V. V. & Thornton, J. M. (2005). Nucleic Acids Res. 33, D266-D268.
32. Lesley, S. A. et al. (2002). Proc. Natl Acad. Sci. USA, 99, 11664-11669.
33. Leslie, A.G.W. (1992). Jnt CCP4/ESF-EACBMNewsl. Protein Crystallogr. 26.
34. Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R. & Gordon, J. I. (2008). Nature Rev. Microbiol. 6, 776-788.
35. Lovell, S. C., Davis, I. W., Arendall, W. B. III, de Bakker, P. I., Word, J. M., Prisant, M. G., Richardson, J. S. & Richardson, D. C. (2003). Proteins, 50, 437-450.
36. Madera, M. (2008). Bioinformatics, 24, 2630-2631.
37. Mai, V. & Draganov, P. V. (2009). World J. Gastroenterol. 15, 81-85.
38. Marchler-Bauer, A. et al. (2007). Nucleic Acids Res. 35, D237-D240.
39. Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
40. McPhillips, T. M., McPhillips, S. E., Chiu, H.-J., Cohen, A. E., Deacon, A. M., Ellis, P. J., Garman, E., Gonzalez, A., Sauter, N. K., Phizackerley, R. P., Soltis, S. M. & Kuhn, P. (2002). J. Synchrotron Rad. 9, 401-406.
41. Nelson, K. E. et al. (2003). J. Bacteriol. 185, 5591-5601.
42. O'Keefe, S. J. (2008). Curr. Opin. Gastroenterol. 24, 51-58.
43. Ochsner, U. A., Vasil, A. I., Johnson, Z. & Vasil, M. L. (1999). J. Bacteriol. 181, 1099-1109.
44. Ordovas, J. M. & Mooser, V. (2006). Curr. Opin. Lipidol. 17, 157-161.
45. Othman, M., Aguero, R. & Lin, H. C. (2008). Curr. Opin. Gastroenterol. 24, 11-16.
46. Reynolds, K. A., Thomson, J. M., Corbett, K. D., Bethel, C. R., Berger, J. M., Kirsch, J. F., Bonomo, R. A. & Handel, T. M. (2006). J. Biol. Chem. 281, 26745-26753.
47. Santarsiero, B. D., Yegian, D. T., Lee, C. C., Spraggon, G., Gu, J., Scheibe, D., Uber, D. C., Cornell, E. W., Nordmeyer, R. A., Kolbe, W. F., Jin, J., Jones, A. L., Jaklevic, J.M., Schultz, P. G. & Stevens, R. C. (2002). J. Appl. Cryst. 35, 278-281.
48. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
49. Sklar, J. G., Wu, T., Gronenberg, L. S., Malinverni, J. C., Kahne, D. & Silhavy, T. J. (2007). Proc. Natl Acad. Sci. USA, 104, 6400-6405.
50. Sleator, R. D., Shortall, C. & Hill, C. (2008). Lett. Appl. Microbiol. 47, 361-366.
51. Strynadka, N. C., Jensen, S. E., Alzari, P. M. & James, M. N. (1996). Nature Struct. Biol. 3, 290-297.
52. Terwilliger, T. C. (2003). Acta Cryst. D59, 38-44.
53. Turnbaugh, P. J., Hamady,M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., Egholm, M., Henrissat, B., Heath, A. C., Knight, R. & Gordon, J. I. (2009). Nature (London), 457, 480-484.
54. Van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L. & Clardy, J. (1993). J. Mol. Biol. 229, 105-124.
55. Vanini, M. M., Spisni, A., Sforca, M. L., Pertinhez, T. A. & Benedetti, C. E. (2008). Proteins, 71, 2051-2064.
56. Verberkmoes, N. C., Russell, A. L., Shah, M., Godzik, A., Rosenquist, M., Halfvarson, J., Lefsrud, M. G., Apajalahti, J., Tysk, C., Hettich, R. L. & Jansson, J. K. (2009). ISME J. 3, 179-189.
57. Vonrhein, C. & Blanc, E. (2007). Methods Mol. Biol. 364, 215-230.
58. Vriend, G. (1990). J. Mol. Graph. 8, 52-56.
59. Winn, M. D., Murshudov, G. N. & Papiz, M. Z. (2003). Methods Enzymol. 374, 300-321.
60. Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K., Chiang, H. C., Hooper, L. V. & Gordon, J. I. (2003). Science, 299, 2074-2076.
61. Xu, J. et al. (2007). PLoS Biol. 5, e156.
62. Yang, H., Guranovic, V., Dutta, S., Feng, Z., Berman, H. M. &Westbrook, J. D. (2004). Acta Cryst. D60, 1833-1839.
63. Ye, Y. & Godzik, A. (2004). Nucleic Acids Res. 32, W582-W585.
64. Yeats, C., Rawlings, N. D. & Bateman, A. (2004). Trends Biochem. Sci. 29, 169-172.
65. Zaneveld, J., Turnbaugh, P. J., Lozupone, C., Ley, R. E., Hamady, M., Gordon, J. I. & Knight, R. (2008). Curr. Opin. Chem. Biol. 12, 109-114.
66. Zhang, M., Monzingo, A. F., Segatori, L., Georgiou, G. & Robertus, J. D. (2004). Acta Cryst. D60, 1512-1518.