A Helical String of Alternately Connected Three-Helix Bundles for the Cell Wall-Associated Adhesion Protein Ebh from Staphylococcus aureus

Structure

Volumn 16, Issue 3, 2008, Pages 488-496

  Tanaka, Yoshikazu ^a,b   Sakamoto, Sou ^b   Kuroda, Makoto ^c   Goda, Shuichiro ^d   Gao, Yong Gui ^a   Tsumoto, Kouhei ^b   Hiragi, Yuzuru ^e   Yao, Min ^a   Watanabe, Nobuhisa ^a   Ohta, Toshiko ^c   Tanaka, Isao ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c UNIVERSITY OF TSUKUBA   (Japan)

^d NAGASAKI UNIVERSITY   (Japan)

^e KANSAI MEDICAL UNIVERSITY   (Japan)

Author keywords

CELLBIO; MICROBIO

Indexed keywords

ARTICLE; CELL ADHESION; CELL STRUCTURE; CELL WALL; CIRCULAR DICHROISM; CRYSTAL STRUCTURE; NONHUMAN; PRIORITY JOURNAL; SPECTROMETRY; STAPHYLOCOCCUS AUREUS; X RAY CRYSTALLOGRAPHY;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CARRIER PROTEINS; CELL ADHESION MOLECULES; CELL WALL; CIRCULAR DICHROISM; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; REPETITIVE SEQUENCES, AMINO ACID; SCATTERING, SMALL ANGLE; SEQUENCE HOMOLOGY, AMINO ACID; STAPHYLOCOCCUS AUREUS; X-RAY DIFFRACTION;

STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS;

EID: 40049083075     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.12.018     Document Type: Article

References (30)

1. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
2. CCP4 (Collaborative Computational Project, Number 4). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50 (1994) 760-763
3. Clarke S.R., Harris L.G., Richards R.G., and Foster S.J. Analysis of Ebh, a 1.1-megadalton cell wall-associated fibronectin-binding protein of Staphylococcus aureus. Infect. Immun. 70 (2002) 6680-6687
4. Cowtan, K. (1994). dm: an automated procedure for phase improvement by density modification. Joint CCP4 and ESFEACBM Newsletter on Protein Crystallography 31, 34-38.
5. Dinges M.M., Orwin P.M., and Schlievert P.M. Exotoxins of Staphylococcus aureus. Clin. Microbiol. Rev. 13 (2000) 16-34
6. Foster T.J., and Hook M. Surface protein adhesins of Staphylococcus aureus. Trends Microbiol. 6 (1998) 484-488
7. Hiragi Y., Sano Y., and Matsumoto T. SAXSANA: an interactive program for the analysis and monitoring of static and time-resolved small-angle X-ray solution scattering measurements. J. Synchrotron Radiat. 10 (2003) 193-196
8. Hiramatsu K. Vancomycin-resistant Staphylococcus aureus: a new model of antibiotic resistance. Lancet Infect. Dis. 1 (2001) 147-155
9. Hiramatsu K., Aritaka N., Hanaki H., Kawasaki S., Hosoda Y., Hori S., Fukuchi Y., and Kobayashi I. Dissemination in Japanese hospitals of strains of Staphylococcus aureus heterogeneously resistant to vancomycin. Lancet 350 (1997) 1670-1673
10. Holden M.T., Feil E.J., Lindsay J.A., Peacock S.J., Day N.P., Enright M.C., Foster T.J., Moore C.E., Hurst L., Atkin R., et al. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc. Natl. Acad. Sci. USA 101 (2004) 9786-9791
11. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
12. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A 32 (1976) 922-923
13. Kajiwara K., and Hiragi Y. Structure analysis by small-angle X-ray scattering. In: Goshi Y. (Ed). Applications of Synchrotron Radiation to Material Analysis (1996), Elsevier, Amsterdam 353-404
14. Kuroda M., Ohta T., Uchiyama I., Baba T., Yuzawa H., Kobayashi I., Cui L., Oguchi A., Aoki K., Nagai Y., et al. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357 (2001) 1225-1240
15. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
16. Schuller D.J. MAGICSQUASH: more versatile non-crystallographic averaging with mulitple constraints. Acta Crystallogr. D Biol. Crystallogr. 52 (1996) 425-434
17. Schwarz-Linek U., Werner J.M., Pickford A.R., Gurusiddappa S., Kim J.H., Pilka E.S., Briggs J.A., Gough T.S., Hook M., Campbell I.D., and Potts J.R. Pathogenic bacteria attach to human fibronectin through a tandem β-zipper. Nature 423 (2003) 177-181
18. Sheldrick G.M., Hauptman H.A., Weeks C.M., Miller R., and Uson I. Ab initio phasing. In: Arnold E. (Ed). International Tables for Crystallography Volume F (2001), Kluwer Academic Publishers, Dordrecht 333-351
19. Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25 (1992) 495-503
20. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76 (1999) 2879-2886
21. Svergun D.I., Petoukhov M.V., and Koch M.H. Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 80 (2001) 2946-2953
22. Terwilliger T.C. Maximum-likelihood density modification. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 965-972
23. Terwilliger T.C. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 38-44
24. Terwilliger T.C. Automated side-chain model building and sequence assignment by template matching. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 45-49
25. Ueki T., Hiragi Y., Izumi Y., Tagawa H., Kataoka M., Muroga Y., Matsushita T., and Amemiya Y. Dynamic behavior of biopolymers by small-angle X-ray scattering (I). Photone Factory Activity Report 1982/1983 Vol. VI (1983) 70-71
26. Ueki T., Hiragi Y., Kataoka M., Inoko Y., Amemiya Y., Izumi Y., Tagawa H., and Muroga Y. Aggregation of bovine serum albumin upon cleavage of its disulfide bonds, studied by the time-resolved small-angle X-ray scattering technique with synchrotron radiation. Biophys. Chem. 23 (1985) 115-124
27. Wang B.C. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115 (1985) 90-112
28. Williams R.J., Henderson B., Sharp L.J., and Nair S.P. Identification of a fibronectin-binding protein from Staphylococcus epidermidis. Infect. Immun. 70 (2002) 6805-6810
29. Yao D.Q., Huang S., Wang J.W., Gu Y.X., Zheng C.D., Fan H.F., Watanabe N., and Tanaka I. SAD phasing by OASIS-2004: case studies of dual-space fragment extension. Acta Crystallogr. D Biol. Crystallogr. 62 (2006) 883-890
30. Yao M., Zhou Y., and Tanaka I. LAFIRE: software for automating the refinement process of protein-structure analysis. Acta Crystallogr. D Biol. Crystallogr. 62 (2006) 189-196