Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: The first structural representative of a new protein family that may play a role in carbohydrate metabolism

Acta Crystallographica Section F: Structural Biology and Crystallization Communications

Volumn 66, Issue 10, 2010, Pages 1287-1296

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

^a Joint Center for Structural Genomics   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

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

^d UNIVERSITY OF CALIFORNIA   (United States)

^e BURNHAM INSTITUTE   (United States)

^f SCRIPPS RESEARCH INSTITUTE   (United States)

^g SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

gut microbiome; immunoglobulin like fold; jelly roll fold; structural genomics; sugars

Indexed keywords

BACTERIAL PROTEIN; CARBOHYDRATE;

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

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BACTEROIDES; BINDING SITES; CARBOHYDRATE METABOLISM; CARBOHYDRATES; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

BACTERIA (MICROORGANISMS); BACTEROIDES THETAIOTAOMICRON; BACTEROIDETES;

EID: 77958071564     PISSN: 17443091     EISSN: 17443091     Source Type: Journal    
DOI: 10.1107/S1744309110028228     Document Type: Article

References (51)

1. Abou-Hachem, M., Karlsson, E. N., Simpson, P. J., Linse, S., Sellers, P., Williamson, M. P., Jamieson, S. J., Gilbert, H. J., Bolam, D. N. & Holst, O. (2002). Biochemistry, 41, 5720-5729.
2. Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J. P., Chothia, C. & Murzin, A. G. (2004). Nucleic Acids Res. 32, D226-D229.
3. Bae, B., Ohene-Adjei, S., Kocherginskaya, S.,Mackie, R. I., Spies,M. A., Cann, I. K. O. & Nair, S. K. (2008). J. Biol. Chem. 283, 12415-12425.
4. Bolam, D. N., Ciruela, A., McQueen-Mason, S., Simpson, P.,Williamson, M. P., Rixon, J. E., Boraston, A., Hazlewood, G. P. & Gilbert, H. J. (1998). Biochem. J. 331, 775-781.
5. Boraston, A. B., Bolam, D. N., Gilbert, H. J. & Davies, G. J. (2004). Biochem. J. 382, 769-781.
6. Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V. & Henrissat, B. (2009). Nucleic Acids Res. 37, D233-D238.
7. Carvalho, A. L., Goyal, A., Prates, J. A. M., Bolam, D. N., Gilbert, H. J., Pires, V. M. R., Ferreira, L. M. A., Planas, A., Romao, M. J. & Fontes, C. (2004). J. Biol. Chem. 279, 34785-34793.
8. Charnock, S. J., Bolam, D. N., Nurizzo, D., Szabo, L., McKie, V. A., Gilbert, H. J. & Davies, G. J. (2002). Proc. Natl Acad. Sci. USA, 99, 14077-14082.
9. 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.
10. Cohen, A. E., Ellis, P. J., Miller, M. D., Deacon, A. M. & Phizackerley, R. P. (2002). J. Appl. Cryst. 35, 720-726.
11. Cohen, S. X., Morris, R. J., Fernandez, F. J., Ben Jelloul, M., Kakaris, M., Parthasarathy, V., Lamzin, V. S., Kleywegt, G. J. & Perrakis, A. (2004). Acta Cryst. D60, 2222-2229.
12. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
13. Comstock, L. E. & Coyne, M. J. (2003). Bioessays, 25, 926-929.
14. Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
15. Czjzek, M., Bolam, D. N., Mosbah, A., Allouch, J., Fontes, C., Ferreira, L. M. A., Bornet, O., Zamboni, V., Darbon, H., Smith, N. L., Black, G. W., Henrissat, B. & Gilbert, H. J. (2001). J. Biol. Chem. 276, 48580-48587.
16. Davies, G. & Henrissat, B. (1995). Structure, 3, 853-859.
17. Davies, G. J., Gloster, T. M. & Henrissat, B. (2005). Curr. Opin. Struct. Biol. 15, 637-645.
18. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
19. Gaskell, A., Crennell, S. & Taylor, G. (1995). Structure, 3, 1197-1205.
20. Gloster, T. M., Turkenburg, J. P., Potts, J. R., Henrissat, B. & Davies, G. J. (2008). Chem. Biol. 15, 1058-1067.
21. Hashimoto, H. (2006). Cell. Mol. Life Sci. 63, 2954-2967.
22. Henrissat, B. & Davies, G. (1997). Curr. Opin. Struct. Biol. 7, 637-644.
23. Keitel, T., Simon, O., Borriss, R. & Heinemann, U. (1993). Proc. Natl Acad. Sci. USA, 90, 5287-5291.
24. Kleywegt, G. J. (2000). Acta Cryst. D56, 249-265.
25. Klock, H. E., Koesema, E. J., Knuth, M.W. & Lesley, S. A. (2008). Proteins, 71, 982-994.
26. Koshland, D. E. (1953). Biol. Rev. Camb. Philos. Soc. 28, 416-436.
27. Krishna, S. S.,Weekes, D., Bakolitsa, C., Elsliger, M.-A.,Wilson, I. A., Godzik, A. & Wooley, J. (2010). Acta Cryst. F66, 1143-1147.
28. Krissinel, E. & Henrick, K. (2007). J. Mol. Biol. 372, 774-797.
29. Landau, M.,Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T. & Ben-Tal, N. (2005). Nucleic Acids Res. 33, W299-W302.
30. Laskowski, R. A. (2009). Nucleic Acids Res. 37, D355-D359
31. Lesley, S. A. et al. (2002). Proc. Natl Acad. Sci. USA, 99, 11664-11669.
32. Leslie, A. G.W. (1992). Jnt CCP4/ESF-EACBM Newsl. Protein Crystallogr. 26.
33. Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
34. 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.
35. Najmudin, S., Guerreiro, C., Carvalho, A. L., Prates, J. A.M., Correia, M. A. S., Alves, V. D., Ferreira, L. M. A., Romao, M. J., Gilbert, H. J., Bolam, D. N. & Fontes, C. (2006). J. Biol. Chem. 281, 8815-8828.
36. Notenboom, V., Boraston, A. B., Kilburn, D. G. & Rose, D. R. (2001). Biochemistry, 40, 6248-6256.
37. Painter, J. & Merritt, E. A. (2006). Acta Cryst. D62, 439-450.
38. 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.
39. Sauve, V., Bruno, S., Berks, B. C. & Hemmings, A. M. (2007). J. Biol. Chem. 282, 23194-23204.
40. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
41. Sinnott, M. L. (1990). Chem. Rev. 90, 1171-1202.
42. Terwilliger, T. (2004). J. Synchrotron Rad. 11, 49-52.
43. Tomme, P., Warren, R. A. & Gilkes, N. R. (1995). Adv. Microb. Physiol. 37, 1-81.
44. Vonrhein, C., Blanc, E., Roversi, P. & Bricogne, G. (2007). Methods Mol. Biol. 364, 215-230.
45. Vriend, G. (1990). J. Mol. Graph. 8, 52-56.
46. Winn, M. D., Murshudov, G. N. & Papiz, M. Z. (2003). Methods Enzymol. 374, 300-321.
47. 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.
48. Yang, H., Guranovic, V., Dutta, S., Feng, Z., Berman, H. M. & Westbrook, J. D. (2004). Acta Cryst. D60, 1833-1839.
49. Ye, Y. & Godzik, A. (2004). Protein Sci. 13, 1841-1850.
50. Yu, X., Visweswaran, G. R., Duck, Z., Marupakula, S., MacIntyre, S., Knight, S. D. & Zavialov, A. V. (2009). Biochem. J. 418, 541-551.
51. Zocco, M. A., Ainora, M. E., Gasbarrini, G. & Gasbarrini, A. (2007). Dig. Liver Dis. 39, 707-712.