Difference between revisions of "Carbohydrate Binding Module Family 80"

Revision as of 04:05, 8 August 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
https://www.cazy.org/CBM80.html

Ligand specificities

CBM80 is a small bacterial family comprising around 96 amino acids and identified in the Ruminococcus flavefaciens cellulosome [1]. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80_RfGH5-1/2, and CBM80_RfGH5) with endo-β1,4-glucanases activity. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity. The only family member characterized is CBM80_RfGH5-1/2 and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) [2]. CBM80_RfGH5-1/2 binds galactomannan in addition to the β-glucans with affinities in the range of 10⁴ to 10⁵ M^-1. Additionally, this CBM binds mannotetraose and not cellotetraose.

Structural Features

The three-dimensional structure of CBM80_RfGH51/2 (5fu3 5fu3) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein. The apo structure of CBM80_RfGH51/2 (Figure 1) and in complex with mannohexaose and cellohexaose was solved to a resolution of 1.0 Å, 1.4 Å and 1.5 Å respectively [2]. CBM80_RfGH51/2 has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) [2]. The β-sheet 2 of CBM80_RfGH51/2 presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490. The mannohexaose-CBM80_RfGH51/2 complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 [2]. The structure of CBM80_RfGH51/2 in complex with cellohexaose revealed electron density for only three glucose units [2].

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 | PubMed ID:18838391 [Cantarel2009]
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.
[DaviesSinnott2008]
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 | PubMed ID:15214846 [Boraston2004]
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 | PubMed ID:17131061 [Hashimoto2006]
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 | PubMed ID:16760304 [Shoseyov2006]
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 | PubMed ID:19908036 [Guillen2010]
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 | PubMed ID:28547780 [Armenta2017]

All Medline abstracts: PubMed

@@ Line 19: / Line 19: @@
 CBM80 is a small bacterial family comprising around 96 amino acids and identified in the Ruminococcus flavefaciens cellulosome <cite>RinconMT2010</cite>. CBM80 displays specificity for β-1,4- and mixed linked β-1,3-1,4-glucans, with some members also binding to β-1,4-mannans. CBM80 is a component of an enzyme that contains catalytic module derived from GH5_4 (CBM80<sub>RfGH5-1/2</sub>, and CBM80<sub>RfGH5</sub>) with endo-β1,4-glucanases activity. CBM80 is also component of an enzyme that contains GH5_7 catalytic module with β1,4-mannanase activity. The only family member characterized is CBM80<sub>RfGH5-1/2</sub> and the dual specificity of this CBM is consistent with the catalytic modules of the enzymes that hydrolyze β-glucans (GH5_4) or β-mannans (GH5_7) <cite>VendittoI2016</cite>. CBM80<sub>RfGH5-1/2</sub> binds galactomannan in addition to the β-glucans with affinities in the range of 10<sup>4</sup> to 10<sup>5</sup> M<sup>-1</sup>.  Additionally, this CBM binds mannotetraose and not cellotetraose.
 == Structural Features ==
-The three-dimensional structure of CBM80<sub>RfGH51/2</sub> ([{{PDBlink}} 5FU3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein. The apo structure of CBM80<sub>RfGH51/2</sub> (Figure 1) and in complex with mannohexaose and cellohexaose was solved to a resolution of 1.0 Å, 1.4 Å and 1.5 Å  respectively <cite>VendittoI2016</cite>. CBM80<sub>RfGH51/2</sub> has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) <cite>VendittoI2016</cite>. The β-sheet 2 of CBM80<sub>RfGH51/2</sub> presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490. The mannohexaose-CBM80<sub>RfGH51/2</sub> complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 <cite>VendittoI2016</cite>. The structure of CBM80<sub>RfGH51/2</sub> in complex with cellohexaose revealed electron density for only three glucose units <cite>VendittoI2016</cite>.
+The three-dimensional structure of CBM80<sub>RfGH51/2</sub> ([{{PDBlink}} 5fu3 5fu3]) was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein. The apo structure of CBM80<sub>RfGH51/2</sub> (Figure 1) and in complex with mannohexaose and cellohexaose was solved to a resolution of 1.0 Å, 1.4 Å and 1.5 Å  respectively <cite>VendittoI2016</cite>. CBM80<sub>RfGH51/2</sub> has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) <cite>VendittoI2016</cite>. The β-sheet 2 of CBM80<sub>RfGH51/2</sub> presents a planar hydrophobic surface with a parallel orientation of Trp453 and Trp489 and a perpendicular orientation of a third aromatic residue, Trp490. The mannohexaose-CBM80<sub>RfGH51/2</sub> complex revealed electron density for mannohexaose along the hydrophobic surface of β-sheet 2 <cite>VendittoI2016</cite>. The structure of CBM80<sub>RfGH51/2</sub> in complex with cellohexaose revealed electron density for only three glucose units <cite>VendittoI2016</cite>.
 == Functionalities ==
 ''Content in this section should include, in paragraph form, a description of:''