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J. Biol. Chem., Vol. 280, Issue 17, 17243-17250, April 29, 2005
The Crystal Structures of EAP Domains from Staphylococcus aureus Reveal an Unexpected Homology to Bacterial Superantigens*![]() ¶![]() ![]() ![]() **
From the
Received for publication, November 1, 2004 , and in revised form, January 31, 2005.
The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 Å resolution, respectively. These structures reveal a core fold that is comprised of an -helix lying diagonally across a five-stranded, mixed -sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the -chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.
Staphylococcus aureus is a widespread, persistent pathogen that causes a broad range of diseases in humans and animals, from simple wound infections to more severe conditions such as septicemia, endocarditis, and osteomyelitis (2). As is the case with many pathogens, initiation of S. aureus infection requires colonization of unique microenvironments within the host. To facilitate host colonization, S. aureus expresses a diverse array of virulence-determining factors, including exoenzymes, toxins, and numerous protein adhesins. These adhesins (termed Receptins (3, 4) or MSCRAMMs (4) (for microbial surface components recognizing adhesive matrix molecules)) are believed to contribute to the initiation and propagation of infections by precluding bacterial clearance by physical forces (e.g. blood flow, coughing, etc.) and providing protection against host immune responses (4).
Although different receptins bind a variety of ligands in host tissues, a common feature is their ability to bind specifically to the large glycoproteins present in the extracellular matrix (e.g. fibronectin, collagen, and fibrinogen) (reviewed in Ref. 5). The 5070-kDa Eap (extracellular adherence protein) of S. aureus was originally identified based on its ability to bind glomerular basement membranes (6), and more mechanistic studies have demonstrated that Eap is capable of binding a wide array of extracellular matrix proteins (79), including fibronectin, vitronectin, laminin, and the pro-inflammatory cell surface receptor intercellular adhesion molecule 1 (ICAM-1) (10). Despite the fact that the mature Eap protein lacks a transmembrane region,
Like many extracellular proteins, Eap exhibits a modular architecture and is believed to be comprised of tandem repeats of an
As a first step toward a molecular understanding of EAP domain-mediated protein-protein interactions, we determined the three-dimensional structures of three distinct EAP domain proteins to 1.8, 2.2, and 1.35 Å resolution, respectively. These structures consist of a 97-residue core fold composed primarily of a long
Molecular Cloning and Sequence Analysis S. aureus strain Mu50 was purchased from ATCC and subcultured in liquid LB medium using standard techniques. Genomic DNA was isolated from 1 liter of stationary phase bacteria according to the procedure originally described by Marmur (20), with the exception that lysostaphin (Sigma) was included in the lysis buffer according to the manufacturer's suggestions. The crude preparation of genomic DNA was purified further by standard extraction and precipitation techniques and resuspended in double distilled H2O to a final concentration of 1.0 mg/ml (A260/A280 = 1.7). The genes encoding EapH1 (GenBankTM accession number NP_372729 [GenBank] ) and EapH2 (GenBankTM accession number NP_371505 [GenBank] ) were identified in the Mu50 genomic sequence by BLAST searching with entire amino acid sequence of Eap (GenBankTM accession number NP_372462 [GenBank] ). The conceptual translation of each gene was analyzed for the highest probability signal peptide cleavage site using the SignalP algorithm Gram-positive option (www.cbs.dtu.dk/services/SignalP/). DNAs encoding residues 31141 of EapH1, residues 24144 of EapH2, and residues 160254 of Eap (the second EAP repeat, denoted EAP2) were amplified by PCR from Mu50 genomic DNA with SalI and NotI restriction endonuclease recognition sites at the 5' and 3' ends, respectively, subcloned into the corresponding sites of the pT7HMT Escherichia coli expression vector,2 and sequenced in their entirety.
Site-directed mutagenesis was used to insert additional methionine residues in the EapH1 protein to facilitate phasing by multiwavelength anomalous dispersion (MAD) (22). The codons for Val91, Ile96, Leu106, and Val116 were mutated independently to encode methionine by a two-step, megaprimer method to create four independent proteins with single-site methionine substitutions (23). Mutant DNAs encoding each variant protein were subcloned into pT7HMT and sequenced in their entirety. All of the sequence alignments were performed using the DNASTAR software suite.
Protein Overexpression and Purification The purified EAP domain fusion proteins were digested with recombinant TEV protease (Invitrogen) at 4 °C according to the manufacturer's suggestions) to avoid potential crystallization problems caused by the presence of the N-terminal fusion tag. When digestion was complete (as judged by SDS-PAGE), the samples were exchanged into 20 mM sodium formate (pH 3.5), applied to a 6-ml Resource S cation exchange column (Amersham Biosciences), washed free of loosely bound contaminants, and eluted with a gradient from 0 to 1 M NaCl over 10 column volumes. Fractions containing apparently homogenous EapH1, EapH2, or EAP2 were pooled, dialyzed once overnight against 4 liters of double distilled H2O using a 3500 molecular weight cut-off Slidealyzer cassette (Pierce Biotechnology), and lyophilized for storage. For overexpression of selenomethionyl-derivatized mutant proteins, selective M9 minimal medium containing 50 mg/liter of seleno-L-methionine (Sigma) was prepared and used according to the general procedure of Beneken et al. (25). Each derivatized protein was purified from the cells in 1 liter of induced culture according to the same protocol used for native proteins, with the exception that all of the buffers were vacuum-degassed prior to use. The incorporation of selenomethionine in each mutant was complete as judged by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (PerkinElmer Life Sciences).
Crystallization and Data Collection
EapH130 mg/ml protein was mixed with a reservoir buffer of 0.1 M sodium cacodylate (pH 6.7), 0.2 M zinc acetate, and 24% (w/v) polyethylene glycol 8000. Twinned, needle-like crystals appeared in 34 days and continued to grow through 14 days. Diffraction quality crystals were grown by microseeding fragments of the needle crystals into identical drops that had been pre-equilibrated for 12 h. EapH1 crystals suitable for diffraction analysis grew in the space group P32 (unit cell dimensions: a = b = 38.55 Å, c = 69.23 Å). The diffraction data for MAD phasing were collected at Selenium edge, peak, and remote wavelengths for crystals of the I96M and L106M mutants using Beamline X4A of the National Synchrotron Light Source at Brookhaven National Laboratory. The diffraction data used for high resolution refinement were collected at Beamline 14BM-C of the Advanced Photon Source at Argonne National Laboratory.
EapH230 mg/ml protein was mixed with a reservoir buffer of 0.1 M sodium cacodylate (pH 6.7), 0.2 M ammonium acetate, 30% (w/v) polyethylene glycol 8000, and 4% (w/v) 2,6-hexanediol. Twinned, needle-like crystals appeared within 2 days and achieved their full size in approximately 1 week. Microseeding produced a single crystal that grew in the space group P21 (unit cell dimensions: a = 50.01 Å, b = 31.97 Å, c = 67.98 Å; EAP213 mg/ml protein was mixed with a reservoir buffer of 0.1 M MES (pH 6.4), 0.1 M ammonium sulfate, and 24% (w/v) polyethylene glycol 8000. Single crystals appeared within 1 day, achieved their full size in approximately 1 week, and grew in the space group R3 (unit cell dimensions: a = b = 64.116 Å, c = 141.706 Å) with two molecules in the asymmetric unit. The diffraction data were collected at Beamline X4A of the National Synchrotron Light Source.
Structure Solution and Refinement
The structure of EapH2 was solved by molecular replacement using the program MOLREP and the refined structure of EapH1 as a search model (32, 34). The top two molecular replacement solutions yielded models for both EapH2 molecules in the asymmetric unit, which were then subjected to a single round of simulated annealing prior to building a 2.2 Å limiting resolution initial model of residues 45144 in both polypeptide chains using the program O (30). Several rounds of model rebuilding and water addition, alternated with positional and individual B-factor refinement, yielded the final model. This model consists of residues 42144 for the first protein molecule in the asymmetric unit, residues 45144 for the second protein molecule, and 76 ordered solvent molecules. Superposition of all of the C
The structure of EAP2 was solved by molecular replacement using the CCP4 program MOLREP and a single molecule from the refined structure of EapH2 as a search model (32, 34). The top molecular replacement solutions yielded models for both EAP2 molecules in the asymmetric unit, which were subjected to a single round of rigid body refinement and simulated annealing prior to building a 1.35 Å limiting resolution initial model of residues 160254 in both polypeptide chains using the program O (30). Noncrystallographic symmetry constraints were applied during the early stages of refinement and were removed once the Rfree value dropped below 40%. Several additional rounds of model rebuilding and water addition, alternated with positional and individual B-factor refinement, yielded the final model. This model consists of residues 160254 for both protein molecules in the asymmetric unit, in addition to the residues Gly-Ser-Thr (an artifact of subcloning) at the N terminus, and 304 ordered solvent molecules. Superposition of all C
The Three-dimensional Structures of Three EAP Domains Two uncharacterized EAP domain proteins were identified from S. aureus strain Mu50 by a BLAST search of the nonredundant protein data base for small proteins that contain EAP domains. These proteins, denoted EapH1 (GenBankTM accession number NP_372729 [GenBank] ) and EapH2 (GenBankTM accession number NP_37505), each contain a signal peptide at their N terminus, followed by a unique stretch of 1020 residues and then a single EAP domain. EapH1 and EapH2 share 47% identity with one another and are 35 and 42% identical to the second repeat in the Eap protein (EAP2), respectively (Table I). DNAs encoding the predicted mature forms of each protein, as well as EAP2, were amplified from bacterial genomic DNA, subcloned, and expressed in E. coli. Following purification, EapH1, EapH2, and EAP2 were crystallized by hanging drop vapor diffusion methods (see "Experimental Procedures").
The three-dimensional structure of EapH1 was determined using MAD data collected from crystals of selenomethionyl-substituted protein and refined to 1.8 Å limiting resolution (Fig. 1A and Tables II and III). The refined structure of EapH1 was used as a molecular replacement search model to determine the structure of EapH2, which was refined to 2.2 Å resolution (Fig. 1B and Tables II and III) and itself used as a molecular replacement search model to determine the structure of EAP2 to 1.35 Å resolution (Fig. 1C and Tables II and III). The EAP domain structures consist primarily of a fourturn -helix laying diagonally across one face of a five-stranded, mixed -sheet and resemble an open hand holding a roll of coins (Fig. 1, rotated).
Whereas the structures of all three EAP domains superimpose well (Table IV), two regions on either edge of the -sheet exhibit notable structural divergence between these proteins (Fig. 2). The first of these regions lies between the 1 and 2 strands. In the case of EapH1 and EapH2, a short, additional strand (denoted 1' in Fig. 1, A and B) is found; this element is absent from EAP2, although strand 2 is extended by two residues toward the N terminus in this protein. The second and more significant region of structural divergence is found between strands 5 and 6. In case of EapH1 and EapH2, the 5 6 region consists of an ordered loop that contains a single turn of 310-helix (Fig. 1). This element is positioned roughly in the middle of the loop in EapH1 (Fig. 1A) but immediately follows strand 5 in EapH2 (Fig. 1B). This type of helical turn is not present in the structure of EAP2 (Fig. 1C). In addition to adopting distinct structures, the residues comprising these regions generally exhibit more flexibility as evidenced by above average temperature factors when compared with the remainder of each molecule. In the case of 1 2, these values are 39.9, 39.6, and 30.2 Å2, whereas for 5 6 they are 40.7, 31.1, and 20.6 Å2, where the mean temperature factors for the protein atoms are 30.2, 30.9, and 14.3 Å2 for the EapH1, EapH2, and EAP2 structures, respectively.
EAP Domains Share Unexpected Structural Homology with Bacterial SuperantigensThe EAP domain structures were compared with structures in the Protein Data Bank by using the structural alignment algorithm DALI (35). Surprisingly, this revealed that EAP domains share significant structural homology with the secreted pyrogenic superantigen toxins TSST-1 (Protein Data Bank code 1AW7 [PDB] (36); Z = 10.7), and SEB (Protein Data Bank code 3SEB [PDB] (37); Z = 8.2), both from S. aureus, and SPE-C (Protein Data Bank code 1AN8 [PDB] (38); Z = 9.1) from Streptococcus pyogenes. Members of the superantigen family of proteins are composed of two structurally distinct domains of approximately equal size (39). The N-terminal domain consists primarily of a -barrel structure that is similar to oligosaccharide/oligonucleotide-binding proteins (oligosaccharide-binding fold), whereas the C-terminal domain adopts a -grasp motif that is structurally homologous to EAP domains (Fig. 3A) (39). When comparing the EAP2 and TSST-1 C-terminal domains, 76 of 98 C atoms superimpose within 2.5 Å distance and with an r.m.s.d. of 1.45 Å (Fig. 3, B and C, and Table IV). This level of structural similarity is surprisingly high because a relationship between these classes of proteins cannot be detected by PSI-BLAST.
Comparison of these two protein structures revealed again that two major regions of structural divergence lay within the 1 2 and 5 6 linker regions. Of these, the most striking difference is found between the 5 6 regions, where a longer 5 strand and more protruding loop conformation is seen in TSST-1CTD than in either EapH1, EapH2, or EAP2. Consistent with this observation, structure-based sequence alignment of several superantigen C-terminal domains with a group of EAP domains revealed that the 5 6 linker region is the major site of sequence variation between these classes of proteins (Fig. 3D). In fact, with the exception of TSST-1, each superantigen examined contains an insertion of at least 13 residues in this region relative to EAP domains. This region is involved in mediating interactions between the superantigen SEC2 and the T-cell receptor, supporting the idea that this variable region can be exploited to confer different binding specificities to EAP domains (Fig. 4).
To further our understanding of EAP domain structure and function, we have determined the crystal structures of three EAP domains, including the second repeat from S. aureus Eap. The results presented here represent the first structural characterization of EAP repeat proteins and show that these domains adopt a -grasp fold composed of 97 residues. This fold is shared by the C-terminal domains of bacterial superantigens and establishes the unexpected result that superantigens and EAP domain proteins are members of a diverse superfamily of secreted bacterial toxins and virulence factors. An attractive explanation for this structural and functional relationship is that EAP domains are a modular scaffold ideally suited to the formation of a wide variety of protein-protein interactions. Consistent with this hypothesis, the structural classification of proteins (SCOP) database indicates that the ability to participate in protein-protein interactions is a general feature of -grasp proteins (40) (scop.bic.nus.edu.sg/data/scop.b.e.bi.html). Functionally characterized Eap proteins are composed of multiple copies of the EAP domain, although it is not known whether these domains interact with one another or behave as physically discrete modules. Primary sequence analysis, biochemical data, and the structures presented here support the latter model, however. First, the individual domains in Eap are separated by positively charged, 1014-amino acid stretches that are predicted to be random coil by secondary structure prediction algorithms (e.g. Ph.D. (41) or PSI-PRED (42)). Second, the full-length Eap protein is sensitive to protease treatment and is readily digested into soluble, protease-stable fragments corresponding to individual EAP domains.3 This suggests that these linker residues are solvent-exposed and/or -accessible. Finally, EAP domains assume a fold where the N- and C-terminal residues are located at the opposite sides of the molecule. This topology is ideally suited to linking modular domains in succession and facilitates the formation of extended, rodlike structures. Similar arrangements are seen for fibronectin type III repeats and immunoglobulin domains, which are commonly found in extended arrays (43). This topology, along with the points mentioned above, suggests that individual EAP domains are unlikely to interact with one another in an intramolecular fashion and that each domain acts a distinct binding module to create polyvalent EAP proteins capable of interacting with a wide variety of ligands and surfaces simultaneously. This secreted, molecular "Velcro" could serve to concentrate regions of bacterial growth and ultimately promote the infection of host cell layers. In this respect, one lingering question is whether the individual domains in Eap are responsible for binding to specific ligands or, alternatively, if individual domains are capable of binding a diverse set of ligands.
The homology between EAP domains and the C-terminal domain of bacterial superantigens suggests that the
During the original characterization of S. aureus Eap, Jonsson et al. (15) reported that the individual EAP subdomains share a short region of homology with the N-terminal region of the While solving the EapH1 structure, two unexpected peaks of high electron density were observed at the contacts between neighboring molecules in the crystal lattice. Several lines of evidence, including the bond lengths, tetrahedral geometry, coordinating residues, and presence of zinc ions in the crystallization buffer, suggested that these sites represented structural zinc ions (Fig. 1A). Both heavy atom sites appear well ordered in the final EapH1 model (BZn-1 = 27.8 Å2, BZn-2 = 42.3 Å2, where Bstructure = 32.2 Å2), a result that is consistent with the correct identification of these metal sites.
Zinc ions are have been shown to mediate the formation of superantigen complexes in both crystal lattices and solution, and zinc appears to be required for the biological activity of these toxins (39, 4649). Despite the many similarities between superantigens and EAP domains, zinc does not appear to be serving a conserved physiological role in EAP domain function. First, the zinc-coordinating residues in the EapH1 structure are not conserved in any other of the EAP domains examined (Fig. 3D). Not surprisingly, structural zinc ions were not observed in the EapH2 or EAP2 structure, nor were divalent cations required for crystallization of either of these proteins. Second, although each molecule of EapH1 binds two zinc ions in the structure, EapH1 does not exhibit metal-dependent multimerization under physiologically relevant zinc concentrations ([Zn2+]
* This work was funded by the Howard Hughes Medical Institute. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
The atomic coordinates and structure factors (codes 1YN3, 1YN4, and 1YN5; Refs. 50 and 51) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).
¶ Postdoctoral fellow of the Howard Hughes Medical Institute. Present address: Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5100 Rockhill Rd., Kansas City, MO 64110. ** Assistant Investigator of the Howard Hughes Medical Institute. To whom correspondence should be addressed: Dept. of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe St., Baltimore, MD 21205. Tel.: 410-614-2533; Fax: 410-614-8839; E-mail: dleahy{at}jhmi.edu.
1 The abbreviations used are: TCR, T-cell receptor; MAD, multiwavelength anomalous diffraction; MES, 4-morpholineethanesulfonic acid; r.m.s.d., root mean square deviation.
2 B. V. Geisbrecht, manuscript in preparation.
3 B. V. Geisbrecht and D. J. Leahy, unpublished observations.
We are grateful to the High-Throughput Crystallization Laboratory of the Hauptmann-Woodward Institute (Buffalo, NY) for providing the initial crystals of EAP2. We also thank K. Ramyar, S. Bouyain, R. Porecha, and J. McLellan for assistance with x-ray data collection, R. Abramowitz and X. Yang of Beamline X4-A at the National Synchrotron Light Source for technical assistance during MAD data collection, and M. Bolbat of Bio-CARS Beamline 14BM-C at the Advanced Photon Source for additional native data collection.
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