- Research
- Open Access
Functional analysis of conserved aromatic amino acids in the discoidin domain of Paenibacillus β-1,3-glucanase
- Yueh-Mei Cheng1,
- Feng-Chia Hsieh1, 2 and
- Menghsiao Meng1Email author
https://doi.org/10.1186/1475-2859-8-62
© Cheng et al; licensee BioMed Central Ltd. 2009
- Received: 13 September 2009
- Accepted: 25 November 2009
- Published: 25 November 2009
Abstract
The 190-kDa Paenibacillus β-1,3-glucanase (LamA) contains a catalytic module of the glycoside hydrolase family 16 (GH16) and several auxiliary domains. Of these, a discoidin domain (DS domain), present in both eukaryotic and prokaryotic proteins with a wide variety of functions, exists at the carboxyl-terminus. To better understand the bacterial DS domain in terms of its structure and function, this domain alone was expressed in Escherichia coli and characterized. The results indicate that the DS domain binds various polysaccharides and enhances the biological activity of the GH16 module on composite substrates. We also investigated the importance of several conserved aromatic residues in the domain's stability and substrate-binding affinity. Both were affected by mutations of these residues; however, the effect on protein stability was more notable. In particular, the forces contributed by a sandwiched triad (W1688, R1756, and W1729) were critical for the presumable β-sandwich fold.
Keywords
- Chitin
- Circular Dichroism Spectrum
- Hyphal Length
- Alginate Lyase
- Catalytic Module
Background
The discoidin domain (DS domain) is a structural and functional motif that is appended, singly or in tandem, to various eukaryotic and prokaryotic proteins [1]. The first DS domain was identified in the amoeba Dictyostelium discoideum and described as a lectin with high affinity for galactose and galactose derivatives [2]. It should be noted that the domain is also referred to as F5/8C due to its presence at the carboxyl-terminus of blood coagulation factors V and VIII. The DS domain binds a wide variety of ligand molecules, including phospholipids, carbohydrates, and partner proteins, thus enabling its cognate protein to participate in various physiological functions such as cellular adhesion [3, 4], migration [5], neural development [6, 7], and nutrition assimilation [8, 9]. A subgroup of the domain possessing carbohydrate-binding ability is also classified as the carbohydrate-binding module family 32 (CBM32) [10]. Due to the recent progress of genome projects, the number of CBM32 members has increased significantly over a short period time. However, most of these members have not been functionally characterized.
The structure of several DS domains has been determined and deposited in the PDB [11]. The DS domain comprises approximately 150 amino acid residues, arranged into a β-sandwich fold with several flexible loops. Presumably, the β-sandwich fold is stabilized predominantly by hydrophobic interactions. The variability within the loops has been suggested to account for the diverse binding spectrum of the DS domain [12]. Co-crystallizations of CBM32 members and their ligands, such as the module of Clostridium perfringens N-acetylglucosaminidase with β-galactosyl-1,4-β-N-acetylglucosamine or the module of Micromonospora viridifaciens sialidase with lactose, demonstrate that the protruding loops form the ligand binding site [13, 14].
Recently, a β-1,3-glucanase consisting of 1793 amino acid residues [GenBank: DQ987544] was isolated from Paenibacillus sp. BCRC 17245 and was characterized [15]. This β-1,3-glucanase (referred to as LamA hereafter) is highly modular, containing a signal sequence, three repeats of the S-layer homologous module, a segment with unknown function, a catalytic module of glycoside hydrolase family 16 (GH16), four repeats of CBM4 family, and a F5/8C module from amino- to carboxyl-terminus. Differential properties between two truncated proteins (GH16 and GH16 tagged with the F5/8C module) suggested that the carboxyl-terminal F5/8C has an ability to complex with polysaccharides containing β-1,3-, β-1,3-1,4-, and β-1,4-glucosidic linkages and such ability conferred greater antifungal activities to GH16 on the growth of Candida albicans and Rhizoctonia solani. In addition, the presence of the F5/8C module enhances the hydrolyzing activity of the catalytic module to various polysaccharides. To better understand the F5/8C module in terms of its structure and function, the module alone was expressed in E. coli and characterized biochemically in this study. In addition, functions of several conserved aromatic amino acid residues in the module were investigated by mutagenesis.
Materials and methods
Chemicals
Laminarin, chitin (from crab shells), and lichenan were purchased from Sigma, while Avicel PH101 was purchased from Fluka. The chitin was treated with phosphoric acid prior to use [16].
Plasmids
pET-C and pET-CF were used for expression of the truncated proteins GH16 and the GH16 fused with F5/8C, respectively [15]. To express the F5/8C module, the pET-F plasmid was generated by PCR-based deletion mutagenesis (QuickChange Site-Directed Mutagenesis Kit, Stratagene) using pET-CF as the template. The PCR was conducted for 35 cycles (95°C, 30 s; 60°C, 30 s; 72°C, 6 min) followed by a 10 min extension at 72°C in a 50 μl solution that contained 10 ng pET-CF, 0.32 mM each of the 5'-phosphorylated primers (5'-TATGCAGGGAATACGGTCTCC and 5'-CGAATTCGGATCCTGGCTGTG), 0.2 mM of each of the dNTPs, and 2.5 U of Pfu polymerase. The PCR product was recovered and self-ligated to become pET-F. A similar PCR protocol, with specific divergent primers, was used to create the specific mutation of pET-F for the production of the mutant F5/8C module. The desired mutations were confirmed with ABI Prism 3773 auto sequencer.
Protein preparation
E. coli BL21(DE3) strain, harboring the desired derivatives of pET-F, was grown at 30°C in 500 mL of 2× TY medium (16 g/L tryptone, 10 g/L yeast extract, and 5 g/L NaCl) supplemented with ampicillin 100 μg/mL until the OD600 reached around 1. Isopropyl β-D-1-thiogalactopyranoside (final concentration of 1 mM) was added to the medium and the culture was continued for 7-8 h. The cells were harvested by centrifugation, suspended in 10 mL lysis buffer (20 mM Tris-HCl [pH8.0], 500 mM NaCl, 10% glycerol, 5 mM phenylmethylsulfonyl fluoride, and 5 mM β-mercaptoethanol), and disrupted by ultrasonic treatment. The clarified protein solution was mixed with Ni-NTA resin (Promega) in the presence of 10 mM imidazole. The mixed resin was washed extensively with wash buffer (10 mM phosphate [pH 7.0], 500 mM NaCl, 10% glycerol, and 40 mM imidazole), and the bound protein was eluted with wash buffer containing 500 mM imidazole. The eluted protein was then passed through a Sephacryl S-300 gel filtration column (Hiprep 16/60, Pharmacia) equilibrated with 10 mM sodium acetate [pH 5.8] and 10% glycerol for further analysis and molecular weight estimation. Protein concentration was determined by the Coomassie blue method using bovine serum albumin (BSA) as the standard.
Instrumental analysis
The sedimentation velocity study was carried out with an analytical ultracentrifuge (Beckman Coulter XL-A) at 20°C and 42000 rpm. The concentration of the protein sample was adjusted to an OD280 of 0.5 (0.17 mg/mL) in 10 mM phosphate buffer [pH 7.0] and 10% glycerol. The UV absorption at 280 nm was scanned 200 times in continuous mode and the data were analyzed with Sedfit94 software to obtain the differential concentration distribution c(s).
The circular dichroism (CD) spectrum within the range of 190 to 360 nm was recorded at room temperature using a Jasco J-815 CD spectrometer fitted with a quartz cell of 5 mm path length. The concentration of the protein sample was adjusted to 0.2 mg/mL in a 10 mM phosphate buffer [pH 7.0]. The data were collected using JWSTDA32 software and analyzed with a CONTINLL program in CDPro software. The protein set SP37 was used as the reference during analysis.
Differential scanning calorimetry (DSC) was performed using a calorimeter (N-DSCIII, TA). Measurements were made with a scan rate of 2°C/min over a 20-80°C range, using a sample concentration of 1 mg/mL in the 10 mM phosphate buffer [pH 7.0]. The data were analyzed with CpCalc OLE 2.0 software.
Substrate binding assays
The affinity of the protein to soluble polysaccharides was assayed by affinity electrophoresis [17] in which 0.3% (w/v) laminarin was included in a native 12% polyacrylamide gel (PAGE). Electrophoresis was performed at 80 V at 4°C.
The affinity of the protein for insoluble polysaccharides was determined by a pull-down assay; the protein (20 μg/mL) and substrates at indicated concentrations were mixed in a final volume of 300 μL in a 50 mM sodium acetate buffer [pH 5.8]. After 1 h of shaking at 37°C, the supernatant was recovered by centrifugation at 16,000 × g for 5 min. The pellet was washed once and suspended in 300 μL of the same buffer. The fraction of protein in the supernatant and the pellet was estimated by 12% sodium dodecyl sulfate (SDS)-PAGE and Coomassie blue staining. The apparent binding affinity (K d) of the protein for chitin was calculated using GraFit5 software according to the dependence of the protein fraction bound to chitin on the amounts of chitin used. K d was defined as the amount of chitin required for reaching 1/2 of the maximal binding of the protein.
Antifungal activity assays
Macroconidia of Fusarium oxysporum f. sp. lycopersici and conidia of Glomerella cingulata were washed out from the respective hypha with a 10 mM sodium acetate buffer [pH 5.8] containing 10% glycerol and adjusted to a concentration of 2 × 105/mL. To determine the protein's effect on conidial germination, equal volumes of the conidia solution and protein sample (12.5 μM) were mixed and incubated at 22°C under moisture condition for 16 h. Growth of hypha from the conidia was observed under a light microscope and the hyphal length was measured using Leica Image-ProPlus 4.5 software.
Results
Protein expression and purification
Monomer to dimer ratio of the F5/8C module of LamA. (A) Elution profile of the purified protein using a Sephacryl S-300 column. The Vo indicates the void volume. The estimated molecular masses of the eluted peaks are indicated. (B) Sedimentation velocity studies. The condition for analytical ultracentrifugation and data analysis are described in the Materials and Methods. (C) Glutaraldehyde cross-linking of the purified F5/8C module. The protein (0.65 mg/mL) was treated with 0.05% glutaraldehyde at room temperature for 1 h and resolved on a 12% SDS-PAGE gel. Lanes 1 and 2 contain the protein sample without and with the treatment of glutaraldehyde, respectively. (D) Glutaraldehyde cross-linking of two larger truncated proteins of LamA (CBF and CB3). The proteins (0.3 mg/mL) were treated with 0.05% glutaraldehyde at room temperature for 40 min and resolved on an 8% SDS-PAGE gel. The arrows point to the putative migration zones of monomeric, dimeric, and multimeric CBF after glutaraldehyde treatment.
Polysaccharide-binding activity
Binding of the F5/8C module of LamA to insoluble polysaccharides. The purified protein (20 μg/mL) and the indicate substrate (25 mg/mL) were thoroughly mixed at 37°C for 1 h. The amount of protein remaining in the supernatant (S) and co-precipitating with the substrate (P) were examined by SDS-PAGE.
Antifungal activity
Effects of the truncated proteins derived from LamA on conidial germination. Germination of F. oxysporum macroconidia (A) and G. cingulata conidia (B) in a buffer containing 6.25 μM of either BSA, the GH16 module, the F5/8C module, or the GH16-F5/8C fusion protein. The culture conditions are described in the Materials and Methods. The germination rate (%) and hyphal length (μm) are indicated in panels A and B, respectively.
Mutational effects on protein structure
Amino acid sequence alignment of several DS domains. (A) Schematic representation of the domain organization of LamA. (B) Sequence alignment, based on the ClustalV method, of the F5/8C module of LamA (Psp; GenBank ABJ15796) with that of Paenibacillus fukuinensis chitosanase-glucanase (Pfu; GenBank BAB64835), Cellvibrio japonicus cbp32B (Cja; GenBank ACE83872), Saccharophagus degradans β-1,3-glucanase (Sde; GenBank ABD82184), retinoschisin (Ret; NP_000321), the C2 domain of human coagulation factor V (Fa5; GenBank AAB59401), the C2 domain of human coagulation factor VIII (Fa8; GenBank AAA52484), and the C2 domain of lactadherin of Bos taurus (Lac; NP_788783). Sequence similarities between the DS domain of Psp and Pfu, Cja, Sde, Ret, Fa5, Fa8, and Lac are 39, 36.9, 44.2, 13.0, 13.0, 14.5, and 16.8%, respectively. Conserved residues are shown in bold, while residues mutated in this study are marked with black dots. Sequences that constitute protruding loops in Fa5, Fa8, and Lac are underlined according to PDB code 1CZS, 1D7P, and 3BN6, respectively. Please note these Proteins can be searched and accessed via http://www.ncbi.nlm.nih.gov/sites/entrez?db=Protein&itool=toolbar
The circular dichroism spectra of wild-type and mutant F5/8C modules of LamA. The experimental conditions are described in the Materials and Methods.
Differential scanning microcalorimetric plots of wild-type and mutant F5/8C modules of LamA. The experimental conditions are described in the Materials and Methods.
Mutational effects on polysaccharide-binding activity
Affinity electrophoresis of wild-type and mutant F5/8C modules. The indicated proteins were separated by native 12% PAGE (A) and native PAGE including 0.3% (w/v) laminarin in the separation gel (B). Open arrows point to the migration positions of the wild-type F5/8C module. The relative mobility (RM) of each protein compared with BSA under the given conditions is indicated.
Dependence of the protein fraction bound to chitin on the chitin concentrations. Each of the indicated proteins (20 μg/mL) was thoroughly mixed with chitin at the indicated concentrations at 37°C for 1 h. The fractions of the protein that remaining in the supernatant (S) and co-precipitating with chitin (P) were determined by SDS-PAGE. The apparent binding affinity (K d) was calculated using GraFit5 software. The data were averages from two independent experiments, each with triplicate samples.
Discussion
According to the sequence information, a variety of bacterial glycoside hydrolases have been suggested to have one or more DS modules. These hydrolases include, but are not limited to, α-1,3-glucanase [19], β-1,3-glucanase [15, 20], β-galactosidase [21], cellulase [22], chitosanase [23], α-1,2-mannanase [24], hyaluronidase [25–27], sialidase [28, 29], alginate lyase [30]. Structural and biochemical studies on the modules of M. viridifaciens sialidase [14], Y. enterocolitica polygalacturonic acid-binding protein [31], and C. perfringens N-acetylglucosaminidase [32] have indicated that galactose or its derivatives are the basic units for recognition by family 32 CBMs. In this study, the F5/8C module of LamA was expressed alone in E. coli and was characterized in vitro. The affinity electrophoresis results and the pull-down assays indicated that the F5/8C module can bind to laminarin as well as many other insoluble polysaccharides, including chitin, lichenan, and cellulose, suggesting a wide substrate-binding spectrum of family 32 CBMs.
With the broad binding specificity, the carboxyl-terminal appended F5/8C module should increase the attachment of LamA to its natural substrates, for instance plant and fungal cell walls that often comprise cellulose, pectin, β-1,3-glucan, β-1,3-1,4-glucan, chitin and others. As a consequence, the F5/8C module increases the encountering frequency between the catalytic GH16 module and the β-1,3-glucosidic linkages within the complex substrates. In other words, the F5/8C module should be able to increase the "effective concentration" of the catalytic module on the surface of the substrates. The enhanced antifungal activity of the GH16 module by F5/8C on the growths of C. albican and R. solani[15], and F. oxysporum and G. cingulata (data presented here) support this notion.
A small fraction of the F5/8C module of LamA form dimers. The recombinant lactadherin C2 domain exists as a monomer in solution, but forms a dimer using a part of a β-strand (S7) as the contact area when it was packed in the crystal [33]. A similar result was observed in the crystal structure of the C2 domain of human factor V [34]. These observations suggest that dimerization under certain circumstances, such as high protein concentration, may be a general property of the DS domain. Dimerization of LamA, presumably anchored on cell wall by its S-layer homologous modules, may increase the binding valence of the protein and further increase the binding avidity of the Paenibacillus strain to its assimilated polysaccharides.
The mutations of W1679, W1688, and Y1768 did not cause dramatic changes in the binding affinity of the F5/8C module to chitin. These data suggest that substrate binding is not the primary function of these residues. Otherwise, a much greater impacts would have been expected. For example, mutations of the conserved tryptophan residues of the CBM on Cellulomonas fimi CenA caused 30- to 50-fold decreases in cellulose-binding affinity [35]. Furthermore, mutations of the CBM on Thermotoga maritima Lam16A caused 30- to 150-fold decreases in celluolose-binding [36].
Structure of the C2 domain of human factor V. A ribbon plot is shown highlighting the β-sandwich fold. Side chains labeled W47, W57, Y88, W99, R137, L149 correspond to W2119, W2129, Y2160, W2171, R2209, and L2221 of mature factor V, respectively.
Conclusion
There is increasing documentation that bacterial glycoside hydrolases contain DS domains. However, the properties and functions of this domain are mostly speculative rather than characterized. Therefore, in this study, we characterized the DS domain in LamA of Paenibacillus sp. BCRC 17245. The DS domain can bind a variety of polysaccharides and maximize the inherent catalytic function of LamA. Furthermore, the importance of the conserved aromatic residues in the protein's conformation and stability can be interpreted based on the structure of mammalian DS domains, despite no more than 16% similarity in amino acid sequences between the domains of LamA and mammalian proteins. This suggests that the core of the β-sandwich fold has been conserved while the DS domain has evolved to have various ligand-binding functions. The W-R-W triad is particularly critical for the formation and maintenance of the β-sandwich fold based on the previous study on retinoschisin, crystal structure of mammalian DS domains, and data presented here.
Declarations
Acknowledgements
This work was supported by National Science Council, ROC: NSC 94-2320-B-127-002.
Authors’ Affiliations
References
- Baumgartner S, Hofmann K, Chiquet-Ehrismann R, Bucher P: The discoidin domain family revisited: New members from prokaryotes and a homology-based fold prediction. Protein Science. 1998, 7: 1626-1631. 10.1002/pro.5560070717.View ArticleGoogle Scholar
- Poole S, Finel R, Lamar E: Sequence and expression of the discoidin 1 family in Dictyostelium discoideum. J Mol Biol. 1981, 153: 273-289. 10.1016/0022-2836(81)90278-3.View ArticleGoogle Scholar
- Ensslin MA, Shur BD: Identification of mouse sperm SED1, a bimotif EGF repeat and discoidin-domain protein involved in sperm-egg binding. Cell. 2003, 114: 405-417. 10.1016/S0092-8674(03)00643-3.View ArticleGoogle Scholar
- Shur BD, Ensslin MA, Rodeheffer C: SED1 function during mammalian sperm-egg adhesion. Curr Opin Cell Biol. 2004, 16: 477-485. 10.1016/j.ceb.2004.07.005.View ArticleGoogle Scholar
- Hidai C, Zupancic T, Penta K, Mikhail A, Kawana M, Quertermous EE, Aoka Y, Fukagawa M, Matsui Y, Platika D, Auerbach R, Hogan BLM, Snodgrass R, Quertermous T: Cloning and characterization of developmental endothelial locus-1: an embryonic endothelial cell protein that binds the αvβ 3 integrin receptor. Genes Dev. 1998, 12: 21-33. 10.1101/gad.12.1.21.View ArticleGoogle Scholar
- Gu C, Rodriguez ER, Reimert DV, Shu T, Fritzsch B, Richards LJ, Kolodkin AL, Ginty DD: Neuropilin-1 conveys semaphoring and VEGF signaling during neural and cardiovascular development. Developmental Cell. 2003, 5: 45-57. 10.1016/S1534-5807(03)00169-2.View ArticleGoogle Scholar
- Kawasaki T, Kitsukawa T, Bekku Y, Matsuda Y, Sanbo M, Yagi T, Fujisawa H: A requirement for neuropilin-1 in embryonic vessel formation. Development. 1999, 126: 4895-4902.Google Scholar
- Corfield T: Bacterial sialidases-roles in pathogenicity and nutrition. Glycobiology. 1992, 2: 509-521. 10.1093/glycob/2.6.509.View ArticleGoogle Scholar
- Gaskell A, Crennell S, Taylor G: The three domains of a bacterial sialidase: a β-propeller, an immunoglobulin module and a galactose-binding jelly-roll. Structure. 1995, 3: 1197-1205. 10.1016/S0969-2126(01)00255-6.View ArticleGoogle Scholar
- Carbohydrate-active enzymes. http://www.cazy.org/fam/acc_CBM.html
- RCSB Protein data bank. http://www.rcsb.org/pdb/home/home.do
- Kiedzierska A, Smietana K, Czepczynska H, Otlewski J: Structural similarities and functional diversity of eukaryotic discoidin-like domains. Biochim Biophys Acta. 2007, 1774: 1069-1078.View ArticleGoogle Scholar
- Ficko-Blean E, Boraston AB: The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-β-hexosaminidase with its carbohydrate receptor. J Biol Chem. 2006, 281: 37748-37757. 10.1074/jbc.M606126200.View ArticleGoogle Scholar
- Newstead SL, Watson JN, Bennet AJ, Taylor G: Galactose recognition by the carbohydrate-binding module of a bacterial sialidase. Acta Cryst D. 2005, 61: 1483-1491. 10.1107/S0907444905026132. 10.1107/S0907444905026132.View ArticleGoogle Scholar
- Cheng YM, Hong TY, Liu CC, Meng M: Cloning and functional characterization of a complex endo-β-1, 3-glucanase from Paenibacillus sp. Appl Microbiol Biotechnol. 2009, 81: 1051-1061. 10.1007/s00253-008-1617-9.View ArticleGoogle Scholar
- Tanaka T, Fujiwara S, Nishikori S, Fukui T, Takagi M, Imanaka T: A unique chitinase with dual active sites and triple substrate binding sites from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. Appl Environ Microbiol. 1999, 65: 5338-5344.Google Scholar
- Tomme P, Creagh AL, Kilburn DG, Haynes CA: Interaction of polysaccharides with the N-terminal cellulosebinding domain of Cellulomonas fimi CenC. 1. Binding specificity and calorimetric analysis. Biochemistry. 1996, 35: 13885-13894. 10.1021/bi961185i.View ArticleGoogle Scholar
- Boraston AB, Bolam DN, Gilbert HJ, Davies GJ: Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J. 2004, 382: 769-781. 10.1042/BJ20040892.View ArticleGoogle Scholar
- Yano S, Wakayama M, Tachiki T: Cloning and expression of an α-1, 3-glucanase gene from Bacillus circulans KA-304: the enzyme participates in protoplast formation of Schizophyllum commune. Biosci Biotechnol Biochem. 2006, 70: 1754-1763. 10.1271/bbb.60095.View ArticleGoogle Scholar
- DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE: Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol. 2008, 190: 5455-5463. 10.1128/JB.01701-07.View ArticleGoogle Scholar
- Goulas TK, Goulas AK, Tzortzis G, Gibson GR: Molecular cloning and comparative analysis of four β-galactosidase genes drom Bifidobacterium bifidum NCIMB41171. Appl Microbiol Biotechnol. 2007, 76: 1365-1372. 10.1007/s00253-007-1099-1.View ArticleGoogle Scholar
- Grant S, Sorokin DY, Grant WD, Jones BE, Heaphy S: A phylogenetic analysis of Wadi el Natrun soda lake cellulose enrichment cultures and identification of cellulase genes from these cultures. Extremophiles. 2004, 8: 421-429. 10.1007/s00792-004-0402-7.View ArticleGoogle Scholar
- Kimoto H, Kusaoke H, Yamamoto I, Fujii Y, Onodera T, Taketo A: Biochemical and genetic properties of Paenibacillus glycosyl hydrolase having chitosanase activity and discoidin domain. J Biol Chem. 2002, 277: 14695-14702. 10.1074/jbc.M108660200.View ArticleGoogle Scholar
- Maruyama Y, Nakajima T, Ichishima E: A 1, 2-α-mannosidase from a Bacillus sp.: purification, characterization, and mode of action. Carbohydrate Res. 1994, 251: 89-98. 10.1016/0008-6215(94)84278-7.View ArticleGoogle Scholar
- Canard B, Garnier T, Saint-Joanis B, Cole ST: Molecular genetic analysis of the nagH gene encoding a hyaluronidase of Clostridium perfringens. Mol Gen Genet. 1994, 243: 215-224.Google Scholar
- Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, Shiba T, Ogasawara N, Hattori M, Kuhara S, Hayashi H: Complete genome sequence of Clostridium perfrigens, an anaerobic flesh-eater. Proc Natl Acad Sci. 2002, 99: 996-1001. 10.1073/pnas.022493799.View ArticleGoogle Scholar
- Brown DR, Zacher LA, Farmerie WG: Spreading factors of Mycoplasma alligatoris, a flesh-eating mycoplasma. J Bacteriol. 2004, 186: 3922-3927. 10.1128/JB.186.12.3922-3927.2004.View ArticleGoogle Scholar
- Rothe B, Rothe B, Roggentin P, Schauer R: The sialidase gene from Clostridium septicum : cloning, sequencing, expression in Escherichia coli and identification of conserved sequences in sialidases and other proteins. Mol Gen Genet. 1991, 226: 190-197. 10.1007/BF00273603.View ArticleGoogle Scholar
- Boraston AB, Ficko-Blean E, Healey M: Carbohydrate recognition by a large sialidase toxin from Clostridium perfringens. Biochemistry. 2007, 46: 11352-11360. 10.1021/bi701317g.View ArticleGoogle Scholar
- Weiner RM, Taylor LE, Henrissat B, Hauser L, Land M, Coutinho PM, Rancurel C, Saunders EH, Longmire AG, Zhang H, Bayer EA, Gilbert HJ, Larimer F, Zhulin IB, Ekborg NA, Lamed R, Richardson PM, Borovok I, Hutcheson S: Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40. PLoS Genetics. 2008, 4: e1000087- 10.1371/journal.pgen.1000087.View ArticleGoogle Scholar
- Abbott DW, Hrynuik S, Boraston AB: Identification and characterization of a novel periplasmic polygalacturonic acid binding protein from Yersinia enterocolitica. J Mol Biol. 2007, 367: 1023-1033. 10.1016/j.jmb.2007.01.030.View ArticleGoogle Scholar
- Ficko-Blean E, Boraston AB: N -acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH. J Mol Biol. 2009, 390: 208-220. 10.1016/j.jmb.2009.04.066.View ArticleGoogle Scholar
- Lin L, Huai Q, Huang M, Furie B, Furie BC: Crystal structure of the bovine lactadherin C2 domain, a membrane binding motif, shows similarity to the C2 domains of factor V and factor VIII. J Mol Biol. 2007, 371: 717-724. 10.1016/j.jmb.2007.05.054.View ArticleGoogle Scholar
- Macedo-Ribeiro S, Bode W, Huber R, Quinn-Allen MA, Kim SW, Ortel TL, Bourenkov GP, Bartunik HD, Stubbs MT, Kane WH, Fuentes-Prior P: Crystal structures of the membrane-binding C2 domain of human coagulation factor V. Nature. 1999, 402: 434-439. 10.1038/46594.View ArticleGoogle Scholar
- Din N, Forsythe IJ, Burtnick LD, Gilkes NR, Miller RC, Warren AJ, Kilburn DG: The cellulose-binding domain of endoglucanase A from Cellulomonas fimi : evidence for the involvement of tryptophan residues in binding. Mol Microbiol. 1994, 11: 747-755. 10.1111/j.1365-2958.1994.tb00352.x.View ArticleGoogle Scholar
- Boraston AB, Warren RA, Kilburn DG: β-1, 3-Glucan binding by a thermostable carbohydrate-binding module from Thermotoga maritima. Biochemistry. 2001, 40: 14679-14685. 10.1021/bi015760g.View ArticleGoogle Scholar
- Fraternali F, Cavallo L, Musco G: Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin. FEBS Letters. 2003, 544: 21-26. 10.1016/S0014-5793(03)00433-2.View ArticleGoogle Scholar
- Lee CC, Kreusch A, McMullan D, Ng K, Spraggon G: Crystal structure of the human neuropilin-1 b1 domain. Structure. 2003, 11: 99-108. 10.1016/S0969-2126(02)00941-3.View ArticleGoogle Scholar
Copyright
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.