Structure of the Streptococcus pneumoniae Surface Protein and Adhesin PfbA

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Suits, Michael D ^a   Boraston, Alisdair B ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; AROMATIC AMINO ACID; BACTERIAL PROTEIN; MEMBRANE PROTEIN; PLASMIN AND FIBRONECTIN BINDING PROTEIN A; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOHYDRATE METABOLISM; CATALYSIS; CRYSTAL STRUCTURE; ENZYME SUBSTRATE; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STREPTOCOCCUS PNEUMONIAE; X RAY CRYSTALLOGRAPHY;

ADHESINS, BACTERIAL; CARBOHYDRATE METABOLISM; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STREPTOCOCCUS PNEUMONIAE;

EID: 84880661396     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067190     Document Type: Article

References (46)

1. Perez-Dorado I, Galan-Bartual S, Hermoso JA, (2012) Pneumococcal surface proteins: when the whole is greater than the sum of its parts. Molecular Oral Microbiology 27: 221-245.
2. Pallen MJ, Lam AC, Antonio M, Dunbar K, (2001) An embarrassment of sortases- a richness of substrates? Trends Microbiol 9: 97-102.
3. Lofling J, Vimberg V, Battig P, Henriques-Normark B, (2011) Cellular interactions by LPxTG-anchored pneumococcal adhesins and their streptococcal homologues. Cell Microbiol 13: 186-197.
4. Paterson GK, Orihuela CJ, (2010) Pneumococcal microbial surface components recognizing adhesive matrix molecules targeting of the extracellular matrix. Mol Microbiol 77: 1-5.
5. Agarwal V, Kuchipudi A, Fulde M, Riesbeck K, Bergmann S, et al. (2013) Streptococcus pneumoniae endopeptidase O (PepO): a multifunctional plasminogen and fibronectin binding protein, facilitating evasion of innate immunity and invasion of host cells. J Biol Chem.
6. Yamaguchi M, Terao Y, Mori Y, Hamada S, Kawabata S, (2008) PfbA, a novel plasmin- and fibronectin-binding protein of Streptococcus pneumoniae, contributes to fibronectin-dependent adhesion and antiphagocytosis. J Biol Chem 283: 36272-36279.
7. Kelley LA, Sternberg MJ, (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4: 363-371.
8. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, et al. (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37: D233-D238.
9. Rozeboom HJ, Bjerkan TM, Kalk KH, Ertesvag H, Holtan S, et al. (2008) Structural and mutational characterization of the catalytic A-module of the mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii. J Biol Chem 283: 23819-23828.
10. Michel G, Chantalat L, Fanchon E, Henrissat B, Kloareg B, et al. (2001) The iota-carrageenase of Alteromonas fortis. A β-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide. J Biol Chem 276: 40202-40209.
11. Barbirz S, Muller JJ, Uetrecht C, Clark AJ, Heinemann U, et al. (2008) Crystal structure of Escherichia coli phage HK620 tailspike: podoviral tailspike endoglycosidase modules are evolutionarily related. Mol Microbiol 69: 303-316.
12. Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, et al. (2004) The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery. J Biol Chem 279: 32882-32896.
13. Jung WS, Hong CK, Lee S, Kim CS, Kim SJ, et al. (2007) Structural and functional insights into intramolecular fructosyl transfer by inulin fructotransferase. J Biol Chem 282: 8414-8423.
14. Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW, (2004) The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J Biol Chem 279: 9139-9145.
15. Emsley P, Charles IG, Fairweather NF, Isaacs NW, (1996) Structure of Bordetella pertussis virulence factor P.69 pertactin. Nature 381: 90-92.
16. Charnock SJ, Brown IE, Turkenburg JP, Black GW, Davies GJ, (2002) Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proc Natl Acad Sci U S A 99: 12067-12072.
17. Garron ML, Cygler M, (2010) Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology 20: 1547-1573.
18. Borgstahl GE, (2007) How to use dynamic light scattering to improve the likelihood of growing macromolecular crystals. Methods Mol Biol 363: 109-129.
19. VanOudenhove J, Anderson E, Krueger S, Cole JL, (2009) Analysis of PKR structure by small-angle scattering. J Mol Biol 387: 910-920.
20. Rambo RP, Tainer JA, (2011) Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers 95: 559-571.
21. Guinier A, Fournet G (1955) Small-angle scattering of X-rays (structure of matter series). New York: Wiley.
22. Jacques DA, Trewhella J, (2010) Small-angle scattering for structural biology-expanding the frontier while avoiding the pitfalls. Protein Sci 19: 642-657.
23. Svergun DI, (1992) Determination of the Regularization Parameter in Indirect-Transform Methods Using Perceptual Criteria. Journal of Applied Crystallography 25: 495-503.
24. Fischer H, Neto MD, Napolitano HB, Polikarpov I, Craievich AF, (2010) Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale. Journal of Applied Crystallography 43: 101-109.
25. Franke D, Svergun DI, (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. Journal of Applied Crystallography 42: 342-346.
26. Ficko-Blean E, Boraston AB, (2012) Insights into the recognition of the human glycome by microbial carbohydrate-binding modules. Curr Opin Struct Biol 22: 570-577.
27. Buckwalter CM, King SJ, (2012) Pneumococcal carbohydrate transport: food for thought. Trends Microbiol 20: 517-522.
28. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
29. Roy A, Kucukural A, Zhang Y, (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5: 725-738.
30. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36: W465-469.
31. Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298.
32. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, et al. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299-302.
33. Studier FW, (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41: 207-234.
34. Robb CS, Nano FE, Boraston AB, (2010) Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of intracellular growth locus E (IglE) protein from Francisella tularensis subsp. novicida. Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1596-1598.
35. Leslie AG, (2006) The integration of macromolecular diffraction data. Acta CrystallogrDBiolCrystallogr 62: 48-57.
36. Evans P, (2006) Scaling and assessment of data quality. Acta CrystallogrDBiolCrystallogr 62: 72-82.
37. Vonrhein C, Blanc E, Roversi P, Bricogne G, (2006) Automated Structure Solution With autoSHARP. Methods MolBiol 364: 215-230.
38. Langer G, Cohen SX, Lamzin VS, Perrakis A, (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3: 1171-1179.
39. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta CrystallogrDBiolCrystallogr 60: 2126-2132.
40. Murshudov GN, Vagin AA, Dodson EJ, (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta CrystallogrDBiolCrystallogr 53: 240-255.
41. McCoy AJ, (2007) Solving structures of protein complexes by molecular replacement with Phaser. Acta CrystallogrDBiolCrystallogr 63: 32-41.
42. Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12-21.
43. Pluvinage B, Chitayat S, Ficko-Blean E, Abbott DW, Kunjachen JM, et al. (2013) Conformational Analysis of StrH, the Surface-Attached exo-β-d-N-Acetylglucosaminidase from Streptococcus pneumoniae. J Mol Biol 425: 334-349.
44. Volkov VV, Svergun DI, (2003) Uniqueness of ab initio shape determination in small-angle scattering. Journal of Applied Crystallography 36: 860-864.
45. Petoukhov MV, Svergun DI, (2005) Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J 89: 1237-1250.
46. Svergun D, Barberato C, Koch MHJ, (1995) CRYSOL- A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. Journal of Applied Crystallography 28: 768-773.