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Difference between revisions of "Carbohydrate Binding Module Family 79"
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== Ligand specificities == | == Ligand specificities == | ||
| − | CBM79 is a family identified in the Ruminococcus flavefaciens cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls <cite>RinconMT2010</cite>. Two CBM79s (CBM79-1<sub> | + | CBM79 is a family identified in the Ruminococcus flavefaciens cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls <cite>RinconMT2010</cite>. Two CBM79s (CBM79-1<sub>RfGH9</sub> and CBM79-2<sub>RfGH9</sub>) were identified in an enzyme that contains a catalytic module derived from GH9 with endo-β1,4-glucanases activity. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans <cite>VendittoI2016</cite>. The ligand binding of CBM79-1<sub>RfGH9</sub> was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays <cite>VendittoI2016</cite>. CBM79-1<sub>RfGH9</sub> binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains. CBM79-1<sub>RfGH9</sub> binds regenerated (noncrystalline) insoluble cellulose (RC) with a K<sub>A</sub> of 4.8 x 10<sup>4</sup> M<sup>-1</sup> . |
== Structural Features == | == Structural Features == | ||
| − | + | The structure of CBM79-1<sub>RfGH9</sub> was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å. CBM79-1<sub>RfGH9</sub> has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) <cite>VendittoI2016</cite>. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1RfGH9 form a twisted hydrophobic platform. In CBM79-1<sub>RfGH9</sub>, the concave surface forms an unusually solvent exposed cleft or planar surface, with loops connecting β-strands 1 and 2 and β-strands 4 and 5 strongly contributing to the curved topology of β-sheet 2. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition, adopting a planar orientation in CBM79-1<sub>RfGH9</sub>. | |
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== Functionalities == | == Functionalities == | ||
Revision as of 09:31, 6 March 2018
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author: ^^^Immacolata Venditto^^^
- Responsible Curator: ^^^Harry Gilbert^^^
| CAZy DB link | |
| http://www.cazy.org/CBM79.html |
Ligand specificities
CBM79 is a family identified in the Ruminococcus flavefaciens cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls [1]. Two CBM79s (CBM79-1RfGH9 and CBM79-2RfGH9) were identified in an enzyme that contains a catalytic module derived from GH9 with endo-β1,4-glucanases activity. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans [2]. The ligand binding of CBM79-1RfGH9 was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays [2]. CBM79-1RfGH9 binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains. CBM79-1RfGH9 binds regenerated (noncrystalline) insoluble cellulose (RC) with a KA of 4.8 x 104 M-1 .
Structural Features
The structure of CBM79-1RfGH9 was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å. CBM79-1RfGH9 has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) [2]. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1RfGH9 form a twisted hydrophobic platform. In CBM79-1RfGH9, the concave surface forms an unusually solvent exposed cleft or planar surface, with loops connecting β-strands 1 and 2 and β-strands 4 and 5 strongly contributing to the curved topology of β-sheet 2. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition, adopting a planar orientation in CBM79-1RfGH9.
Functionalities
Content in this section should include, in paragraph form, a description of:
- Functional role of CBM: Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
- Most Common Associated Modules: 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
- Novel Applications: Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.
Family Firsts
- First Identified
- Insert archetype here, possibly including very brief synopsis.
- First Structural Characterization
- Insert archetype here, possibly including very brief synopsis.
References
- Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |
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Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. The Biochemist, vol. 30, no. 4., pp. 26-32. Download PDF version.
- Boraston AB, Bolam DN, Gilbert HJ, and Davies GJ. (2004). Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J. 2004;382(Pt 3):769-81. DOI:10.1042/BJ20040892 |
- Hashimoto H (2006). Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci. 2006;63(24):2954-67. DOI:10.1007/s00018-006-6195-3 |
- Shoseyov O, Shani Z, and Levy I. (2006). Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev. 2006;70(2):283-95. DOI:10.1128/MMBR.00028-05 |
- Guillén D, Sánchez S, and Rodríguez-Sanoja R. (2010). Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol. 2010;85(5):1241-9. DOI:10.1007/s00253-009-2331-y |
- Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, and Rodríguez-Sanoja R. (2017). Advances in molecular engineering of carbohydrate-binding modules. Proteins. 2017;85(9):1602-1617. DOI:10.1002/prot.25327 |