Crystal structures of Bbp from Staphylococcus aureus reveal the ligand binding mechanism with Fibrinogen α

Abstract

Bone sialoprotein-binding protein (Bbp), a MSCRAMMs (Microbial Surface Components Recognizing Adhesive Matrix Molecules) family protein expressed on the surface of Staphylococcus aureus (S. aureus), mediates adherence to fibrinogen α (Fg α), a component in the extracellular matrix of the host cell and is important for infection and pathogenesis. In this study, we solved the crystal structures of apo-Bbp^273−598 and Bbp^273−598-Fg α^561−575 complex at a resolution of 2.03 Å and 1.45 Å, respectively. Apo-Bbp^273−598 contained the ligand binding region N2 and N3 domains, both of which followed a DE variant IgG fold characterized by an additional D1 strand in N2 domain and D1′ and D2′ strands in N3 domain. The peptide mapped to the Fg α^561−575 bond to Bbp^273−598 on the open groove between the N2 and N3 domains. Strikingly, the disordered C-terminus in the apo-form reorganized into a highly-ordered loop and a β-strand G′′ covering the ligand upon ligand binding. Bbp^{Ala298−Gly301} in the N2 domain of the Bbp^273−598-Fg α^561−575 complex, which is a loop in the apo-form, formed a short α-helix to interact tightly with the peptide. In addition, Bbp^{Ser547−Gln561} in the N3 domain moved toward the binding groove to make contact directly with the peptide, while Bbp^{Asp338−Gly355} and Bbp^{Thr365−Tyr387} in N2 domain shifted their configurations to stabilize the reorganized C-terminus mainly through strong hydrogen bonds. Altogether, our results revealed the molecular basis for Bbp-ligand interaction and advanced our understanding of S. aureus infection process.

Keywords

bone sialoprotein-binding protein (Bbp) / fibrinogen / serine-aspartate repeat (Sdr) / Microbial Surface Components Recognizing Adhesive Matrix Molecules (MSCRAMM) / Staphylococcus aureus

References

[1] Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58: 1948−1954

[2] Davis SL, Gurusiddappa S, McCrea KW, Perkins S, Hook M (2001) SdrG, a fibrinogen-binding bacterial adhesin of the microbial surface components recognizing adhesive matrix molecules subfamily from Staphylococcus epidermidis, targets the thrombin cleavage site in the Bbeta chain. J Biol Chem 276: 27799−27805

[3] Deivanayagam C, Wann ER, Chen W, Carson M, Rajashankar KR, Höök M, Narayana SV (2002) A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor A. EMBO J 21: 6660−6672

[4] Deresinski S, Herrera V (2010) Immunotherapies for Staphylococcus aureus: current challenges and future prospects. Infect Control Hosp Epidemiol 31(Suppl 1): S45−47

[5] Downer R, Roche F, Park PW, Mecham RP, Foster TJ (2002) The elastin-binding protein of Staphylococcus aureus (EbpS) is expressed at the cell surface as an integral membrane protein and not as a cell wall-associated protein. J Biol Chem 277: 243−250

[6] Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126−2132

[7] Gailit J, Clarke C, Newman D, Tonnesen MG, Mosesson MW, Clark RA (1997) Human fibroblasts bind directly to fibrinogen at RGD sites through integrin αvβ3. Exp Cell Res 232: 118−126

[8] Ganesh VK, Rivera JJ, Smeds E, Ko YP, Bowden MG, Wann ER, Gurusiddappa S, Fitzgerald JR, Hook M (2008) A structural model of the Staphylococcus aureus ClfA-fibrinogen interaction opens new avenues for the design of anti-staphylococcal therapeutics. PLoS Pathog 4: e1000226

[9] Ganesh VK, Barbu EM, Deivanayagam CC, Le B, Anderson AS, Matsuka YV, Lin SL, Foster TJ, Narayana SV, Hook M (2011) Structural and biochemical characterization of Staphylococcus aureus clumping factor B/ligand interactions. J Biol Chem 286: 25963−25972

[10] Ganss B, Kim RH, Sodek J (1999) Bone sialoprotein. Crit Rev Oral Biol Med 10: 79−98

[11] Gillaspy AF, Lee CY, Sau S, Cheung AL, Smeltzer MS (1998) Factors affecting the collagen binding capacity of Staphylococcus aureus. Infect Immun 66: 3170−3178

[12] Hultenby K, Reinholt FP, Norgard M, Oldberg A, Wendel M, Heinegard D (1994) Dephosphorylation of osteopontin and bone sialoprotein by osteoclastic tartrate-resistant acid phosphatase. Eur J Cell Biol 63: 230−239

[13] Hunter GK, Goldberg HA (1993) Nucleation of hydroxyapatite by bone sialoprotein. Proc Natl Acad Sci USA 90: 8562−8565

[14] Jancarik J, Scott WG, Milligan DL, Koshland DE, Kim S-H (1991) Crystallization and preliminary X-ray diffraction study of the ligand-binding domain of the bacterial chemotaxis-mediating aspartate receptor of Salmonella typhimurium. J Mol Biol 221: 31−34

[15] Josefsson E, McCrea KW, Ni Eidhin D, O’Connell D, Cox J, Hook M, Foster TJ (1998) Three new members of the serine-aspartate repeat protein multigene family of Staphylococcus aureus. Microbiology 144(Pt 12): 3387−3395

[16] Kluytmans J, van Belkum A, Verbrugh H (1997) Nasal carriage of Staphylococcus aureus: epidemiology, underlying mechanisms, and associated risks. Clin Microbiol Rev 10: 505−520

[17] Kollman JM, Pandi L, Sawaya MR, Riley M, Doolittle RF (2009) Crystal structure of human fibrinogen. Biochemistry 48: 3877−3886

[18] Lowy FD (1998) Staphylococcus aureus infections. N Engl J Med 339: 520−532

[19] McCrea KW, Hartford O, Davis S, Eidhin DN, Lina G, Speziale P, Foster TJ, Hook M (2000) The serine-aspartate repeat (Sdr) protein family in Staphylococcus epidermidis. Microbiology 146( Pt 7): 1535−1546

[20] McDevitt D, Francois P, Vaudaux P, Foster TJ (1994) Molecular characterization of the clumping factor (fibrinogen receptor) of Staphylococcus aureus. Mol Microbiol 11: 237−248

[21] Mosesson MW, Siebenlist KR, Meh DA (2001) The structure and biological features of fibrinogen and fibrin. Ann N Y Acad Sci 936: 11−30

[22] Ni Eidhin D, Perkins S, Francois P, Vaudaux P, Hook M, Foster TJ (1998) Clumping factor B (ClfB), a new surface-located fibrinogen-binding adhesin of Staphylococcus aureus. Mol Microbiol 30: 245−257

[23] Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol 276: 307−326

[24] Patti JM, Allen BL, McGavin MJ, Hook M (1994) MSCRAMMmediated adherence of microorganisms to host tissues. Annu Rev Microbiol 48: 585−617

[25] Peacock SJ, Moore CE, Justice A, Kantzanou M, Story L, Mackie K, O’Neill G, Day NP (2002) Virulent combinations of adhesin and toxin genes in natural populations of Staphylococcus aureus. Infect Immun 70: 4987−4996

[26] Ponnuraj K, Bowden MG, Davis S, Gurusiddappa S, Moore D, Choe D, Xu Y, Hook M, Narayana SV (2003) A “dock, lock, and latch” structural model for a staphylococcal adhesin binding to fibrinogen. Cell 115: 217−228

[27] Rivera J, Vannakambadi G, Hook M, Speziale P (2007) Fibrinogenbinding proteins of Gram-positive bacteria. Thromb Haemost 98: 503−511

[28] Ryden C, Maxe I, Franzen A, Ljungh A, Heinegard D, Rubin K (1987) Selective binding of bone matrix sialoprotein to Staphylococcus aureus in osteomyelitis. Lancet 2: 515

[29] Tung H, Guss B, Hellman U, Persson L, Rubin K, Ryden C (2000) A bone sialoprotein-binding protein from Staphylococcus aureus: a member of the staphylococcal Sdr family. Biochem J 345(Pt 3): 611−619

[30] Vazquez V, Liang X, Horndahl JK, Ganesh VK, Smeds E, Foster TJ, Hook M (2011) Fibrinogen is a ligand for the Staphylococcus aureus microbial surface components recognizing adhesive matrix molecules (MSCRAMM) bone sialoprotein-binding protein (Bbp). J Biol Chem 286: 29797−29805

[31] Wang X, Ge J, Liu B, Hu Y, Yang M (2013) Structures of SdrD from Staphylococcus aureus reveal the molecular mechanism of how the cell surface receptors recognize their ligands. Protein Cell 4: 277−285

[32] Wann ER, Gurusiddappa S, Hook M (2000) The fibronectin-binding MSCRAMM FnbpA of Staphylococcus aureus is a bifunctional protein that also binds to fibrinogen. J Biol Chem 275: 13863−13871

[33] Xiang H, Feng Y, Wang J, Liu B, Chen Y, Liu L, Deng X, Yang M (2012) Crystal structures reveal the multi-ligand binding mechanism of Staphylococcus aureus ClfB. PLoS pathog 8: e1002751

[34] Zetola N, Francis JS, Nuermberger EL, Bishai WR (2005) Community-acquired meticillin-resistant Staphylococcus aureus: an emerging threat. Lancet Infect Dis 5: 275−286

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